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Antonopoulos A, Gilleard JS, Charlier J. Next-generation sequencing technologies for helminth diagnostics and surveillance in ruminants: shifting diagnostic barriers. Trends Parasitol 2024; 40:511-526. [PMID: 38760257 DOI: 10.1016/j.pt.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/19/2024]
Abstract
Helminth infections in grazing ruminants are a major issue for livestock farming globally, but are unavoidable in outdoor grazing systems and must be effectively managed to avoid deleterious effects to animal health, and productivity. Next-generation sequencing (NGS) technologies are transforming our understanding of the genetic basis of anthelmintic resistance (AR) and epidemiological studies of ruminant gastrointestinal parasites. They also have the potential to not only help develop and validate molecular diagnostic tests but to be directly used in routine diagnostics integrating species-specific identification and AR into a single test. Here, we review how these developments have opened the pathway for the development of multi-AR and multispecies identification in a single test, with widespread implications for sustainable livestock farming for the future.
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Affiliation(s)
- Alistair Antonopoulos
- Kreavet, Kruibeke, Belgium; School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, UK.
| | - John S Gilleard
- Faculty of Veterinary Medicine, Host-Parasite Interactions Program, University of Calgary, Calgary, Alberta, Canada
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2
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Antonopoulos A, Charvet CL, Maitland K, Doyle SR, Neveu C, Laing R. Functional validation of novel levamisole resistance marker S168T in Haemonchus contortus. Int J Parasitol Drugs Drug Resist 2024; 24:100524. [PMID: 38346379 PMCID: PMC10867575 DOI: 10.1016/j.ijpddr.2024.100524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/18/2024]
Abstract
Recently, a S168T variant in the acetylcholine receptor subunit ACR-8 was associated with levamisole resistance in the parasitic helminth Haemonchus contortus. Here, we used the Xenopus laevis oocyte expression system and two-electrode voltage-clamp electrophysiology to measure the functional impact of this S168T variant on the H. contortus levamisole-sensitive acetylcholine receptor, L-AChR-1.1. Expression of the ACR-8 S168T variant significantly reduced the current amplitude elicited by levamisole compared to acetylcholine, with levamisole changing from a full to partial agonist on the recombinant L-AChR. Functional validation of the S168T mutation on modulating levamisole activity at the receptor level highlights its critical importance as both a mechanism and a marker of levamisole resistance.
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Affiliation(s)
- Alistair Antonopoulos
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom; Kreavet, Kruibeke, Belgium.
| | | | - Kirsty Maitland
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Stephen R Doyle
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | | | - Roz Laing
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom
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3
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Jung H, Zarlenga D, Martin JC, Geldhof P, Hallsworth-Pepin K, Mitreva M. The identification of small molecule inhibitors with anthelmintic activities that target conserved proteins among ruminant gastrointestinal nematodes. mBio 2024; 15:e0009524. [PMID: 38358246 PMCID: PMC10936192 DOI: 10.1128/mbio.00095-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Gastrointestinal nematode (GIN) infections are a major concern for the ruminant industry worldwide and result in significant production losses. Naturally occurring polyparasitism and increasing drug resistance that potentiate disease outcomes are observed among the most prevalent GINs of veterinary importance. Within the five major taxonomic clades, clade Va represents a group of GINs that predominantly affect the abomasum or small intestine of ruminants. However, the development of effective broad-spectrum anthelmintics against ruminant clade Va GINs has been challenged by a lack of comprehensive druggable genome resources. Here, we first assembled draft genomes for three clade Va species (Cooperia oncophora, Trichostrongylus colubriformis, and Ostertagia ostertagi) and compared them with closely related ruminant GINs. Genome-wide phylogenetic reconstruction showed a relationship among ruminant GINs structured by taxonomic classification. Orthogroup (OG) inference and functional enrichment analyses identified 220 clade Va-specific and Va-conserved OGs, enriched for functions related to cell cycle and cellular senescence. Further transcriptomic analysis identified 61 taxonomically and functionally conserved clade Va OGs that may function as drug targets for new broad-spectrum anthelmintics. Chemogenomic screening identified 11 compounds targeting homologs of these OGs, thus having potential anthelmintic activity. In in vitro phenotypic assays, three kinase inhibitors (digitoxigenin, K-252a, and staurosporine) exhibited broad-spectrum anthelmintic activities against clade Va GINs by obstructing the motility of exsheathed L3 (xL3) or molting of xL3 to L4. These results demonstrate valuable applications of the new ruminant GIN genomes in gaining better insights into their life cycles and offer a contemporary approach to discovering the next generation of anthelmintics.IMPORTANCEGastrointestinal nematode (GIN) infections in ruminants are caused by parasites that inhibit normal function in the digestive tract of cattle, sheep, and goats, thereby causing morbidity and mortality. Coinfection and increasing drug resistance to current therapeutic agents will continue to worsen disease outcomes and impose significant production losses on domestic livestock producers worldwide. In combination with ongoing therapeutic efforts, advancing the discovery of new drugs with novel modes of action is critical for better controlling GIN infections. The significance of this study is in assembling and characterizing new GIN genomes of Cooperia oncophora, Ostertagia ostertagi, and Trichostrongylus colubriformis for facilitating a multi-omics approach to identify novel, biologically conserved drug targets for five major GINs of veterinary importance. With this information, we were then able to demonstrate the potential of commercially available compounds as new anthelmintics.
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Affiliation(s)
- Hyeim Jung
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Dante Zarlenga
- Animal Parasitic Diseases Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, USA
| | - John C. Martin
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Peter Geldhof
- Laboratory of Parasitology, Faculty of Veterinary Medicine, University of Ghent, Merelbeke, Belgium
| | | | - Makedonka Mitreva
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, USA
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4
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McKean EL, Grill E, Choi YJ, Mitreva M, O'Halloran DM, Hawdon JM. Altered larval activation response associated with multidrug resistance in the canine hookworm Ancylostoma caninum. Parasitology 2024; 151:271-281. [PMID: 38163962 PMCID: PMC11007283 DOI: 10.1017/s0031182023001385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 01/03/2024]
Abstract
Parasitic gastrointestinal nematodes pose significant health risks to humans, livestock, and companion animals, and their control relies heavily on the use of anthelmintic drugs. Overuse of these drugs has led to the emergence of resistant nematode populations. Herein, a naturally occurring isolate (referred to as BCR) of the dog hookworm, Ancylostoma caninum, that is resistant to 3 major classes of anthelmintics is characterized. Various drug assays were used to determine the resistance of BCR to thiabendazole, ivermectin, moxidectin and pyrantel pamoate. When compared to a drug-susceptible isolate of A. caninum, BCR was shown to be significantly resistant to all 4 of the drugs tested. Multiple single nucleotide polymorphisms have been shown to impart benzimidazole resistance, including the F167Y mutation in the β-tubulin isotype 1 gene, which was confirmed to be present in BCR through molecular analysis. The frequency of the resistant allele in BCR was 76.3% following its first passage in the lab, which represented an increase from approximately 50% in the founding hookworm population. A second, recently described mutation in codon 134 (Q134H) was also detected at lower frequency in the BCR population. Additionally, BCR exhibits an altered larval activation phenotype compared to the susceptible isolate, suggesting differences in the signalling pathways involved in the activation process which may be associated with resistance. Further characterization of this isolate will provide insights into the mechanisms of resistance to macrocyclic lactones and tetrahydropyrimidine anthelmintics.
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Affiliation(s)
- Elise L. McKean
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC, USA
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Emilia Grill
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Young-Jun Choi
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Makedonka Mitreva
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Damien M. O'Halloran
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - John M. Hawdon
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC, USA
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5
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Dube F, Delhomme N, Martin F, Hinas A, Åbrink M, Svärd S, Tydén E. Gene co-expression network analysis reveal core responsive genes in Parascaris univalens tissues following ivermectin exposure. PLoS One 2024; 19:e0298039. [PMID: 38359071 PMCID: PMC10868809 DOI: 10.1371/journal.pone.0298039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
Anthelmintic resistance in equine parasite Parascaris univalens, compromises ivermectin (IVM) effectiveness and necessitates an in-depth understanding of its resistance mechanisms. Most research, primarily focused on holistic gene expression analyses, may overlook vital tissue-specific responses and often limit the scope of novel genes. This study leveraged gene co-expression network analysis to elucidate tissue-specific transcriptional responses and to identify core genes implicated in the IVM response in P. univalens. Adult worms (n = 28) were exposed to 10-11 M and 10-9 M IVM in vitro for 24 hours. RNA-sequencing examined transcriptional changes in the anterior end and intestine. Differential expression analysis revealed pronounced tissue differences, with the intestine exhibiting substantially more IVM-induced transcriptional activity. Gene co-expression network analysis identified seven modules significantly associated with the response to IVM. Within these, 219 core genes were detected, largely expressed in the intestinal tissue and spanning diverse biological processes with unspecific patterns. After 10-11 M IVM, intestinal tissue core genes showed transcriptional suppression, cell cycle inhibition, and ribosomal alterations. Interestingly, genes PgR028_g047 (sorb-1), PgB01_g200 (gmap-1) and PgR046_g017 (col-37 & col-102) switched from downregulation at 10-11 M to upregulation at 10-9 M IVM. The 10-9 M concentration induced expression of cuticle and membrane integrity core genes in the intestinal tissue. No clear core gene patterns were visible in the anterior end after 10-11 M IVM. However, after 10-9 M IVM, the anterior end mostly displayed downregulation, indicating disrupted transcriptional regulation. One interesting finding was the non-modular calcium-signaling gene, PgR047_g066 (gegf-1), which uniquely connected 71 genes across four modules. These genes were enriched for transmembrane signaling activity, suggesting that PgR047_g066 (gegf-1) could have a key signaling role. By unveiling tissue-specific expression patterns and highlighting biological processes through unbiased core gene detection, this study reveals intricate IVM responses in P. univalens. These findings suggest alternative drug uptake of IVM and can guide functional validations to further IVM resistance mechanism understanding.
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Affiliation(s)
- Faruk Dube
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Frida Martin
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Andrea Hinas
- Department of Cell and Molecular Biology, Uppsala University, Uppsala Sweden
| | - Magnus Åbrink
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Staffan Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala Sweden
| | - Eva Tydén
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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6
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Rehborg EG, Wheeler NJ, Zamanian M. Mapping resistance-associated anthelmintic interactions in the model nematode Caenorhabditis elegans. PLoS Negl Trop Dis 2023; 17:e0011705. [PMID: 37883578 PMCID: PMC10629664 DOI: 10.1371/journal.pntd.0011705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 11/07/2023] [Accepted: 10/07/2023] [Indexed: 10/28/2023] Open
Abstract
Parasitic nematodes infect billions of people and are mainly controlled by anthelmintic mass drug administration (MDA). While there are growing efforts to better understand mechanisms of anthelmintic resistance in human and animal populations, it is unclear how resistance mechanisms that alter susceptibility to one drug affect the interactions and efficacy of drugs used in combination. Mutations that alter drug permeability across primary nematode barriers have been identified as potential resistance mechanisms using the model nematode Caenorhabditis elegans. We leveraged high-throughput assays in this model system to measure altered anthelmintic susceptibility in response to genetic perturbations of potential cuticular, amphidial, and alimentary routes of drug entry. Mutations in genes associated with these tissue barriers differentially altered susceptibility to the major anthelmintic classes (macrocyclic lactones, benzimidazoles, and nicotinic acetylcholine receptor agonists) as measured by animal development. We investigated two-way anthelmintic interactions across C. elegans genetic backgrounds that confer resistance or hypersensitivity to one or more drugs. We observe that genetic perturbations that alter susceptibility to a single drug can shift the drug interaction landscape and lead to the appearance of novel synergistic and antagonistic interactions. This work establishes a framework for investigating combinatorial therapies in model nematodes that can potentially be translated to amenable parasite species.
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Affiliation(s)
- Elena G. Rehborg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Nicolas J. Wheeler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Mostafa Zamanian
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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7
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Raza A, Williams AR, Abeer MM. Importance of ABC Transporters in the Survival of Parasitic Nematodes and the Prospect for the Development of Novel Control Strategies. Pathogens 2023; 12:755. [PMID: 37375445 DOI: 10.3390/pathogens12060755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/10/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
ABC transporters, a family of ATP-dependent transmembrane proteins, are responsible for the active transport of a wide range of molecules across cell membranes, including drugs, toxins, and nutrients. Nematodes possess a great diversity of ABC transporters; however, only P-glycoproteins have been well-characterized compared to other classes. The ABC transport proteins have been implicated in developing resistance to various classes of anthelmintic drugs in parasitic nematodes; their role in plant and human parasitic nematodes still needs further investigation. Therefore, ABC transport proteins offer a potential opportunity to develop nematode control strategies. Multidrug resistance inhibitors are becoming more attractive for controlling nematodes due to their potential to increase drug efficacy in two ways: (i) by limiting drug efflux from nematodes, thereby increasing the amount of drug that reaches its target site, and (ii) by reducing drug excretion by host animals, thereby enhancing drug bioavailability. This article reviews the role of ABC transporters in the survival of parasitic nematodes, including the genes involved, their regulation and physiological roles, as well as recent developments in their characterization. It also discusses the association of ABC transporters with anthelmintic resistance and the possibility of targeting them with next-generation inhibitors or nutraceuticals (e.g., polyphenols) to control parasitic infections.
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Affiliation(s)
- Ali Raza
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, St Lucia, QLD 4067, Australia
| | - Andrew R Williams
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Frederiksberg, Denmark
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8
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Rehborg EG, Wheeler NJ, Zamanian M. Mapping resistance-associated anthelmintic interactions in the model nematode Caenorhabditis elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538424. [PMID: 37163071 PMCID: PMC10168335 DOI: 10.1101/2023.04.26.538424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Parasitic nematodes infect billions of people and are mainly controlled by anthelmintic mass drug administration (MDA). While there are growing efforts to better understand mechanisms of anthelmintic resistance in human and animal populations, it is unclear how resistance mechanisms that alter susceptibility to one drug affect the interactions and efficacy of drugs used in combination. Mutations that alter drug permeability across primary nematode barriers have been identified as potential resistance mechanisms using the model nematode Caenorhabditis elegans. We leveraged high-throughput assays in this model system to measure altered anthelmintic susceptibility in response to genetic perturbations of potential cuticular, amphidial, and alimentary routes of drug entry. Mutations in genes associated with these tissue barriers differentially altered susceptibility to the major anthelmintic classes (macrocyclic lactones, benzimidazoles, and nicotinic acetylcholine receptor agonists) as measured by animal development. We investigated two-way anthelmintic interactions across C. elegans genetic backgrounds that confer resistance or hypersensitivity to one or more drugs. We observe that genetic perturbations that alter susceptibility to a single drug can shift the drug interaction landscape and lead to the appearance of novel synergistic and antagonistic interactions. This work establishes a framework for investigating combinatorial therapies in model nematodes that can potentially be translated to amenable parasite species.
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Affiliation(s)
- Elena G. Rehborg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
| | - Nicolas J Wheeler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI USA
| | - Mostafa Zamanian
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI USA
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9
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Labbé F, Abdeladhim M, Abrudan J, Araki AS, Araujo RN, Arensburger P, Benoit JB, Brazil RP, Bruno RV, Bueno da Silva Rivas G, Carvalho de Abreu V, Charamis J, Coutinho-Abreu IV, da Costa-Latgé SG, Darby A, Dillon VM, Emrich SJ, Fernandez-Medina D, Figueiredo Gontijo N, Flanley CM, Gatherer D, Genta FA, Gesing S, Giraldo-Calderón GI, Gomes B, Aguiar ERGR, Hamilton JGC, Hamarsheh O, Hawksworth M, Hendershot JM, Hickner PV, Imler JL, Ioannidis P, Jennings EC, Kamhawi S, Karageorgiou C, Kennedy RC, Krueger A, Latorre-Estivalis JM, Ligoxygakis P, Meireles-Filho ACA, Minx P, Miranda JC, Montague MJ, Nowling RJ, Oliveira F, Ortigão-Farias J, Pavan MG, Horacio Pereira M, Nobrega Pitaluga A, Proveti Olmo R, Ramalho-Ortigao M, Ribeiro JMC, Rosendale AJ, Sant’Anna MRV, Scherer SE, Secundino NFC, Shoue DA, da Silva Moraes C, Gesto JSM, Souza NA, Syed Z, Tadros S, Teles-de-Freitas R, Telleria EL, Tomlinson C, Traub-Csekö YM, Marques JT, Tu Z, Unger MF, Valenzuela J, Ferreira FV, de Oliveira KPV, Vigoder FM, Vontas J, Wang L, Weedall GD, Zhioua E, Richards S, Warren WC, Waterhouse RM, Dillon RJ, McDowell MA. Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World. PLoS Negl Trop Dis 2023; 17:e0010862. [PMID: 37043542 PMCID: PMC10138862 DOI: 10.1371/journal.pntd.0010862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 04/27/2023] [Accepted: 02/13/2023] [Indexed: 04/13/2023] Open
Abstract
Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites.
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Affiliation(s)
- Frédéric Labbé
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | - Maha Abdeladhim
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Jenica Abrudan
- Genomic Sciences & Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Alejandra Saori Araki
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | - Ricardo N. Araujo
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciencias Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Brazil
| | - Peter Arensburger
- Department of Biological Sciences, California State Polytechnic University, Pomona, California, United States of America
| | - Joshua B. Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | | | - Rafaela V. Bruno
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | - Gustavo Bueno da Silva Rivas
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Vinicius Carvalho de Abreu
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jason Charamis
- Department of Biology, University of Crete, Voutes University Campus, Heraklion, Greece
- Molecular Entomology Lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
| | - Iliano V. Coutinho-Abreu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, California, United States of America
| | | | - Alistair Darby
- Institute of Integrative Biology, The University of Liverpool, Liverpool, United Kingdom
| | - Viv M. Dillon
- Institute of Integrative Biology, The University of Liverpool, Liverpool, United Kingdom
| | - Scott J. Emrich
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | | | - Nelder Figueiredo Gontijo
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciencias Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Brazil
| | - Catherine M. Flanley
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | - Derek Gatherer
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, United Kingdom
| | - Fernando A. Genta
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | - Sandra Gesing
- Discovery Partners Institute, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Gloria I. Giraldo-Calderón
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
- Dept. Ciencias Biológicas & Dept. Ciencias Básicas Médicas, Universidad Icesi, Cali, Colombia
| | - Bruno Gomes
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - James G. C. Hamilton
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, United Kingdom
| | - Omar Hamarsheh
- Department of Life Sciences, Faculty of Science and Technology, Al-Quds University, Jerusalem, Palestine
| | - Mallory Hawksworth
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | - Jacob M. Hendershot
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Paul V. Hickner
- USDA-ARS Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, Kerrville, Texas, United States of America
| | - Jean-Luc Imler
- CNRS-UPR9022 Institut de Biologie Moléculaire et Cellulaire and Faculté des Sciences de la Vie-Université de Strasbourg, Strasbourg, France
| | - Panagiotis Ioannidis
- Molecular Entomology Lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
| | - Emily C. Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Shaden Kamhawi
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Charikleia Karageorgiou
- Molecular Entomology Lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
- Genomics Group – Bioinformatics and Evolutionary Biology Lab, Department of Genetics and Microbiology, Autonomous University of Barcelona, Barcelona, Spain
| | - Ryan C. Kennedy
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | - Andreas Krueger
- Medical Entomology Branch, Dept. Microbiology, Bundeswehr Hospital, Hamburg, Germany
- Medical Zoology Branch, Dept. Microbiology, Central Bundeswehr Hospital, Koblenz, Germany
| | - José M. Latorre-Estivalis
- Laboratorio de Insectos Sociales, Instituto de Fisiología, Biología Molecular y Neurociencias, Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Petros Ligoxygakis
- Laboratory of Cell Biology, Development and Genetics, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Patrick Minx
- Donald Danforth Plant Science Center, Olivette, Missouri, United States of America
| | - Jose Carlos Miranda
- Laboratório de Imunoparasitologia, CPqGM, Fundação Oswaldo Cruz, Bahia, Brazil
| | - Michael J. Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ronald J. Nowling
- Department of Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of America
| | - Fabiano Oliveira
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | | | - Marcio G. Pavan
- Laboratório de Bioquímica e Fisiologia de Insetos, IOC, FIOCRUZ, Rio de Janeiro, Brazil
- Laboratório de Transmissores de Hematozoários, IOC, FIOCRUZ, Rio de Janeiro, Brazil
| | - Marcos Horacio Pereira
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciencias Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Brazil
| | - Andre Nobrega Pitaluga
- Laboratório de Biologia Molecular de Parasitas e Vetores, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, Brazil
| | - Roenick Proveti Olmo
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marcelo Ramalho-Ortigao
- F. Edward Hebert School of Medicine, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, United States of America
| | - José M. C. Ribeiro
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Andrew J. Rosendale
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Mauricio R. V. Sant’Anna
- Laboratório de Fisiologia de Insetos Hematófagos, Universidade Federal de Minas Gerais, Instituto de Ciencias Biológicas, Departamento de Parasitologia, Pampulha, Belo Horizonte, Brazil
| | - Steven E. Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | | | - Douglas A. Shoue
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | | | | | - Nataly Araujo Souza
- Laboratory Interdisciplinar em Vigilancia Entomologia em Diptera e Hemiptera, Fiocruz, Rio de Janeiro, Brazil
| | - Zainulabueddin Syed
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Samuel Tadros
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
| | | | - Erich L. Telleria
- Department of Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of America
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | | | - João Trindade Marques
- Department of Biology and Center for Biological Clocks Research, Texas A&M University, College Station, Texas, United States of America
| | - Zhijian Tu
- Fralin Life Science Institute and Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Maria F. Unger
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Jesus Valenzuela
- Vector Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Flávia V. Ferreira
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Karla P. V. de Oliveira
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Felipe M. Vigoder
- Universidade Federal do Rio de Janeiro, Instituto de Biologia. Rio de Janeiro, Brazil
| | - John Vontas
- Molecular Entomology Lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (FORTH), Heraklion, Greece
- Pesticide Science Lab, Department of Crop Science, Agricultural University of Athens, Athens Greece
| | - Lihui Wang
- Donald Danforth Plant Science Center, Olivette, Missouri, United States of America
| | - Gareth D. Weedall
- Vector Biology Department, Liverpool School of Tropical Medicine (LSTM), Liverpool, United Kingdom
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Elyes Zhioua
- Vector Ecology Unit, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wesley C. Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, United States of America
| | - Robert M. Waterhouse
- Department of Ecology & Evolution and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Rod J. Dillon
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, United Kingdom
| | - Mary Ann McDowell
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre dame, Notre Dame, Indiana, United States of America
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10
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Villacis‐Perez E, Xue W, Vandenhole M, De Beer B, Dermauw W, Van Leeuwen T. Intraspecific diversity in the mechanisms underlying abamectin resistance in a cosmopolitan pest. Evol Appl 2023; 16:863-879. [PMID: 37124092 PMCID: PMC10130554 DOI: 10.1111/eva.13542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/28/2023] Open
Abstract
Pesticide resistance relies on a myriad of mechanisms, ranging from single mutations to a complex and polygenic architecture, and it involves mechanisms such as target-site insensitivity, metabolic detoxification, or a combination of these, with either additive or synergistic effects. Several resistance mechanisms against abamectin, a macrocyclic lactone widely used in crop protection, have been reported in the cosmopolitan pest Tetranychus urticae. However, it has been shown that a single mechanism cannot account for the high levels of abamectin resistance found across different mite populations. Here, we used experimental evolution combined with bulked segregant analyses to map quantitative trait loci (QTL) associated with abamectin resistance in two genetically unrelated populations of T. urticae. In these two independent QTL mapping experiments, three and four QTLs were identified, of which three were shared between experiments. Shared QTLs contained genes encoding subunits of the glutamate-gated chloride channel (GluCl) and harboured previously reported mutations, including G314D in GluCl1 and G326E in GluCl3, but also novel resistance candidate loci, including DNA helicases and chemosensory receptors. Surprisingly, the fourth QTL, present only in only one of the experiments and thus unique for one resistant parental line, revealed a non-functional variant of GluCl2, suggesting gene knock-out as resistance mechanism. Our study uncovers the complex basis of abamectin resistance, and it highlights the intraspecific diversity of genetic mechanisms underlying resistance in a cosmopolitan pest.
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Affiliation(s)
- Ernesto Villacis‐Perez
- Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
- Institute for Biodiversity and Ecosystem Dynamics (IBED)University of Amsterdam (UvA)AmsterdamThe Netherlands
| | - Wenxin Xue
- Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Marilou Vandenhole
- Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Berdien De Beer
- Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Wannes Dermauw
- Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
- Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO)MerelbekeBelgium
| | - Thomas Van Leeuwen
- Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
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11
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Shaver AO, Wit J, Dilks CM, Crombie TA, Li H, Aroian RV, Andersen EC. Variation in anthelmintic responses are driven by genetic differences among diverse C. elegans wild strains. PLoS Pathog 2023; 19:e1011285. [PMID: 37011090 PMCID: PMC10101645 DOI: 10.1371/journal.ppat.1011285] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/13/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023] Open
Abstract
Treatment of parasitic nematode infections in humans and livestock relies on a limited arsenal of anthelmintic drugs that have historically reduced parasite burdens. However, anthelmintic resistance (AR) is increasing, and little is known about the molecular and genetic causes of resistance for most drugs. The free-living roundworm Caenorhabditis elegans has proven to be a tractable model to understand AR, where studies have led to the identification of molecular targets of all major anthelmintic drug classes. Here, we used genetically diverse C. elegans strains to perform dose-response analyses across 26 anthelmintic drugs that represent the three major anthelmintic drug classes (benzimidazoles, macrocyclic lactones, and nicotinic acetylcholine receptor agonists) in addition to seven other anthelmintic classes. First, we found that C. elegans strains displayed similar anthelmintic responses within drug classes and significant variation across drug classes. Next, we compared the effective concentration estimates to induce a 10% maximal response (EC10) and slope estimates of each dose-response curve of each strain to the laboratory reference strain, which enabled the identification of anthelmintics with population-wide differences to understand how genetics contribute to AR. Because genetically diverse strains displayed differential susceptibilities within and across anthelmintics, we show that C. elegans is a useful model for screening potential nematicides before applications to helminths. Third, we quantified the levels of anthelmintic response variation caused by genetic differences among individuals (heritability) to each drug and observed a significant correlation between exposure closest to the EC10 and the exposure that exhibited the most heritable responses. These results suggest drugs to prioritize in genome-wide association studies, which will enable the identification of AR genes.
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Affiliation(s)
- Amanda O. Shaver
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Janneke Wit
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Clayton M. Dilks
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Timothy A. Crombie
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Hanchen Li
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Raffi V. Aroian
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Erik C. Andersen
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
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12
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Thorn CS, Maness RW, Hulke JM, Delmore KE, Criscione CD. Population genomics of helminth parasites. J Helminthol 2023; 97:e29. [PMID: 36927601 DOI: 10.1017/s0022149x23000123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.
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Affiliation(s)
- C S Thorn
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - R W Maness
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - J M Hulke
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - K E Delmore
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - C D Criscione
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
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13
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Hassan SU, Chua EG, Paz EA, Tay CY, Greeff JC, Palmer DG, Dudchenko O, Aiden EL, Martin GB, Kaur P. Chromosome-length genome assembly of Teladorsagia circumcincta - a globally important helminth parasite in livestock. BMC Genomics 2023; 24:74. [PMID: 36792983 PMCID: PMC9933375 DOI: 10.1186/s12864-023-09172-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Gastrointestinal (GIT) helminthiasis is a global problem that affects livestock health, especially in small ruminants. One of the major helminth parasites of sheep and goats, Teladorsagia circumcincta, infects the abomasum and causes production losses, reductions in weight gain, diarrhoea and, in some cases, death in young animals. Control strategies have relied heavily on the use of anthelmintic medication but, unfortunately, T. circumcincta has developed resistance, as have many helminths. Vaccination offers a sustainable and practical solution, but there is no commercially available vaccine to prevent Teladorsagiosis. The discovery of new strategies for controlling T. circumcincta, such as novel vaccine targets and drug candidates, would be greatly accelerated by the availability of better quality, chromosome-length, genome assembly because it would allow the identification of key genetic determinants of the pathophysiology of infection and host-parasite interaction. The available draft genome assembly of T. circumcincta (GCA_002352805.1) is highly fragmented and thus impedes large-scale investigations of population and functional genomics. RESULTS We have constructed a high-quality reference genome, with chromosome-length scaffolds, by purging alternative haplotypes from the existing draft genome assembly and scaffolding the result using chromosome conformation, capture-based, in situ Hi-C technique. The improved (Hi-C) assembly resulted in six chromosome-length scaffolds with length ranging from 66.6 Mbp to 49.6 Mbp, 35% fewer sequences and reduction in size. Substantial improvements were also achieved in both the values for N50 (57.1 Mbp) and L50 (5 Mbp). A higher and comparable level of genome and proteome completeness was achieved for Hi-C assembly on BUSCO parameters. The Hi-C assembly had a greater synteny and number of orthologs with a closely related nematode, Haemonchus contortus. CONCLUSION This improved genomic resource is suitable as a foundation for the identification of potential targets for vaccine and drug development.
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Affiliation(s)
- Shamshad Ul Hassan
- grid.1012.20000 0004 1936 7910UWA School of Agriculture and Environment, The University of Western Australia, 6009 Crawley, WA Australia ,grid.1012.20000 0004 1936 7910Helicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA Australia
| | - Eng Guan Chua
- grid.1012.20000 0004 1936 7910Helicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA Australia
| | - Erwin A. Paz
- grid.1012.20000 0004 1936 7910UWA School of Agriculture and Environment, The University of Western Australia, 6009 Crawley, WA Australia ,grid.1012.20000 0004 1936 7910Helicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA Australia
| | - Chin Yen Tay
- grid.1012.20000 0004 1936 7910Helicobacter Research Laboratory, The Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA Australia
| | - Johan C. Greeff
- grid.493004.aDepartment of Primary Industries and Regional Development, Western Australia 3 Baron Hay Court, South Perth, 6151 WA Australia
| | - Dieter G. Palmer
- grid.493004.aDepartment of Primary Industries and Regional Development, Western Australia 3 Baron Hay Court, South Perth, 6151 WA Australia
| | - Olga Dudchenko
- grid.39382.330000 0001 2160 926XThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, 77030 Houston, TX USA ,grid.21940.3e0000 0004 1936 8278Center for Theoretical Biological Physics, Rice University, 77005 Houston, TX USA
| | - Erez Lieberman Aiden
- grid.39382.330000 0001 2160 926XThe Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, 77030 Houston, TX USA ,grid.21940.3e0000 0004 1936 8278Center for Theoretical Biological Physics, Rice University, 77005 Houston, TX USA ,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong China ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Graeme B. Martin
- grid.1012.20000 0004 1936 7910UWA School of Agriculture and Environment, The University of Western Australia, 6009 Crawley, WA Australia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, 6009, Crawley, WA, Australia.
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14
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Dube F, Hinas A, Delhomme N, Åbrink M, Svärd S, Tydén E. Transcriptomics of ivermectin response in Caenorhabditis elegans: Integrating abamectin quantitative trait loci and comparison to the Ivermectin-exposed DA1316 strain. PLoS One 2023; 18:e0285262. [PMID: 37141255 PMCID: PMC10159168 DOI: 10.1371/journal.pone.0285262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Parasitic nematodes pose a significant threat to human and animal health, as well as cause economic losses in the agricultural sector. The use of anthelmintic drugs, such as Ivermectin (IVM), to control these parasites has led to widespread drug resistance. Identifying genetic markers of resistance in parasitic nematodes can be challenging, but the free-living nematode Caenorhabditis elegans provides a suitable model. In this study, we aimed to analyze the transcriptomes of adult C. elegans worms of the N2 strain exposed to the anthelmintic drug Ivermectin (IVM), and compare them to those of the resistant strain DA1316 and the recently identified Abamectin Quantitative Trait Loci (QTL) on chromosome V. We exposed pools of 300 adult N2 worms to IVM (10-7 and 10-8 M) for 4 hours at 20°C, extracted total RNA and sequenced it on the Illumina NovaSeq6000 platform. Differentially expressed genes (DEGs) were determined using an in-house pipeline. The DEGs were compared to genes from a previous microarray study on IVM-resistant C. elegans and Abamectin-QTL. Our results revealed 615 DEGs (183 up-regulated and 432 down-regulated genes) from diverse gene families in the N2 C. elegans strain. Of these DEGs, 31 overlapped with genes from IVM-exposed adult worms of the DA1316 strain. We identified 19 genes, including the folate transporter (folt-2) and the transmembrane transporter (T22F3.11), which exhibited an opposite expression in N2 and the DA1316 strain and were deemed potential candidates. Additionally, we compiled a list of potential candidates for further research including T-type calcium channel (cca-1), potassium chloride cotransporter (kcc-2), as well as other genes such as glutamate-gated channel (glc-1) that mapped to the Abamectin-QTL.
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Affiliation(s)
- Faruk Dube
- Department of Biomedical Sciences and Veterinary Public Health, Division of Parasitology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Andrea Hinas
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Magnus Åbrink
- Department of Biomedical Sciences and Veterinary Public Health, Section of Immunology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Staffan Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Eva Tydén
- Department of Biomedical Sciences and Veterinary Public Health, Division of Parasitology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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15
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Doyle SR, Laing R, Bartley D, Morrison A, Holroyd N, Maitland K, Antonopoulos A, Chaudhry U, Flis I, Howell S, McIntyre J, Gilleard JS, Tait A, Mable B, Kaplan R, Sargison N, Britton C, Berriman M, Devaney E, Cotton JA. Genomic landscape of drug response reveals mediators of anthelmintic resistance. Cell Rep 2022; 41:111522. [PMID: 36261007 PMCID: PMC9597552 DOI: 10.1016/j.celrep.2022.111522] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/11/2022] [Accepted: 09/26/2022] [Indexed: 11/18/2022] Open
Abstract
Like other pathogens, parasitic helminths can rapidly evolve resistance to drug treatment. Understanding the genetic basis of anthelmintic drug resistance in parasitic nematodes is key to tracking its spread and improving the efficacy and sustainability of parasite control. Here, we use an in vivo genetic cross between drug-susceptible and multi-drug-resistant strains of Haemonchus contortus in a natural host-parasite system to simultaneously map resistance loci for the three major classes of anthelmintics. This approach identifies new alleles for resistance to benzimidazoles and levamisole and implicates the transcription factor cky-1 in ivermectin resistance. This gene is within a locus under selection in ivermectin-resistant populations worldwide; expression analyses and functional validation using knockdown experiments support that cky-1 is associated with ivermectin survival. Our work demonstrates the feasibility of high-resolution forward genetics in a parasitic nematode and identifies variants for the development of molecular diagnostics to combat drug resistance in the field.
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Affiliation(s)
- Stephen R Doyle
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.
| | - Roz Laing
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK.
| | - David Bartley
- Moredun Research Institute, Penicuik, Midlothian EH26 0PZ, UK
| | - Alison Morrison
- Moredun Research Institute, Penicuik, Midlothian EH26 0PZ, UK
| | - Nancy Holroyd
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Kirsty Maitland
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Alistair Antonopoulos
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Umer Chaudhry
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Ilona Flis
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Sue Howell
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Jennifer McIntyre
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions Program, Faculty of Veterinary Medicine, University of Calgary, Calgary T2N 1N4, Canada
| | - Andy Tait
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Barbara Mable
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Ray Kaplan
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Neil Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Collette Britton
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | | | - Eileen Devaney
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - James A Cotton
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
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16
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Genomic signatures of selection associated with benzimidazole drug treatments in Haemonchus contortus field populations. Int J Parasitol 2022; 52:677-689. [PMID: 36113620 DOI: 10.1016/j.ijpara.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 11/22/2022]
Abstract
Genome-wide methods offer a powerful approach to detect signatures of drug selection. However, limited availability of suitable reference genomes and the difficulty of obtaining field populations with well-defined, distinct drug treatment histories mean there is little information on the signatures of selection in parasitic nematodes and on how best to detect them. This study addresses these knowledge gaps by using field populations of Haemonchus contortus with well-defined benzimidazole treatment histories, leveraging a recently completed chromosomal-scale reference genome assembly. We generated a panel of 49,393 genomic markers to genotype 20 individual adult worms from each of four H. contortus populations: two from closed sheep flocks with an approximate 20 year history of frequent benzimidazole treatment, and two populations with a history of little or no treatment. Sampling occurred in the same geographical region to limit genetic differentiation and maximise the detection sensitivity. A clear signature of selection was detected on chromosome I, centred on the isotype-1 β-tubulin gene. Two additional, but weaker, signatures of selection were detected; one near the middle of chromosome I spanning 3.75 Mbp and 259 annotated genes, and one on chromosome II spanning a region of 3.3 Mbp and 206 annotated genes, including the isotype-2 β-tubulin locus. We also assessed how sensitivity was impacted by sequencing depth, worm number, and pooled versus individual worm sequence data. This study provides the first known direct genome-wide evidence for any parasitic nematode, that the isotype-1 β-tubulin gene is quantitatively the single most important benzimidazole resistance locus. It also identified two additional genomic regions that likely contain benzimidazole resistance loci of secondary importance. This study provides an experimental framework to maximise the power of genome-wide approaches to detect signatures of selection driven by anthelmintic drug treatments in field populations of parasitic nematodes.
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17
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The equine ascarids: resuscitating historic model organisms for modern purposes. Parasitol Res 2022; 121:2775-2791. [PMID: 35986167 PMCID: PMC9391215 DOI: 10.1007/s00436-022-07627-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/12/2022] [Indexed: 11/23/2022]
Abstract
The equine ascarids, Parascaris spp., are important nematode parasites of juvenile horses and were historically model organisms in the field of cell biology, leading to many important discoveries, and are used for the study of chromatin diminution. In veterinary parasitology, Parascaris spp. are important not only because they can cause clinical disease in young horses but also because they are the only ascarid parasites to have developed widespread anthelmintic resistance. Despite this, much of the general biology and mechanisms of anthelmintic resistance are poorly understood. This review condenses known basic biological information and knowledge on the mechanisms of anthelmintic resistance in Parascaris spp., highlighting the importance of foundational research programs. Although two variants of this parasite were recognized based on the number of chromosomes in the 1870s and suggested to be two species in 1890, one of these, P. univalens, appears to have been largely forgotten in the veterinary scientific literature over the past 100 years. We describe how this omission has had a century-long effect on nomenclature and data analysis in the field, highlighting the importance of proper specimen identification in public repositories. A summary of important basic biology, including life cycle, in vitro maintenance, and immunology, is given, and areas of future research for the improvement of knowledge and development of new systems are given. Finally, the limited knowledge regarding anthelmintic resistance in Parascaris spp. is summarized, along with caution regarding assumptions that resistance mechanisms can be applied across clades.
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Transgenic Expression of Haemonchus contortus Cytochrome P450 Hco-cyp-13A11 Decreases Susceptibility to Particular but Not All Macrocyclic Lactones in the Model Organism Caenorhabditis elegans. Int J Mol Sci 2022; 23:ijms23169155. [PMID: 36012413 PMCID: PMC9409383 DOI: 10.3390/ijms23169155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/24/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
The number of reported macrocyclic lactones (ML) resistance cases across all livestock hosts is steadily increasing. Different studies in the parasitic nematode Haemonchus contortus assume the participation of cytochrome P450s (Cyps) enzymes in ML resistance. Still, functional data about their individual contribution to resistance or substrate specificity is missing. Via microinjection, transgenic Caenorhabditis elegans expressing HCON_00141052 (transgene-Hco-cyp-13A11) from extrachromosomal arrays were generated. After 24 h of exposure to different concentrations of ivermectin (IVM), ivermectin aglycone (IVMa), selamectin (SEL), doramectin (DRM), eprinomectin (EPR), and moxidectin (MOX), motility assays were performed to determine the impact of the H. contortus Cyp to the susceptibility of the worms against each ML. While transgene-Hco-cyp-13A11 significantly decreased susceptibility to IVM (four-fold), IVMa (2-fold), and SEL (3-fold), a slight effect for DRM and no effect for MOX, and EPR was observed. This substrate specificity of Hco-cyp-13A11 could not be explained by molecular modeling and docking studies. Hco-Cyp-13A11 molecular models were obtained for alleles from isolates with different resistance statuses. Although 14 amino acid polymorphisms were detected, none was resistance specific. In conclusion, Hco-cyp-13A11 decreased IVM, IVMa, and SEL susceptibility to a different extent, but its potential impact on ML resistance is not driven by polymorphisms.
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Antonopoulos A, Doyle SR, Bartley DJ, Morrison AA, Kaplan R, Howell S, Neveu C, Busin V, Devaney E, Laing R. Allele specific PCR for a major marker of levamisole resistance in Haemonchus contortus. Int J Parasitol Drugs Drug Resist 2022; 20:17-26. [PMID: 35970104 PMCID: PMC9399269 DOI: 10.1016/j.ijpddr.2022.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 12/14/2022]
Abstract
Haemonchus contortus is a haematophagous parasitic nematode that infects small ruminants and causes significant animal health concerns and economic losses within the livestock industry on a global scale. Treatment primarily depends on broad-spectrum anthelmintics, however, resistance is established or rapidly emerging against all major drug classes. Levamisole (LEV) remains an important treatment option for parasite control, as resistance to LEV is less prevalent than to members of other major classes of anthelmintics. LEV is an acetylcholine receptor (AChR) agonist that, when bound, results in paralysis of the worm. Numerous studies implicated the AChR sub-unit, ACR-8, in LEV sensitivity and in particular, the presence of a truncated acr-8 transcript or a deletion in the acr-8 locus in some resistant isolates. Recently, a single non-synonymous SNP in acr-8 conferring a serine-to-threonine substitution (S168T) was identified that was strongly associated with LEV resistance. Here, we investigate the role of genetic variation at the acr-8 locus in a controlled genetic cross between the LEV susceptible MHco3(ISE) and LEV resistant MHco18(UGA2004) isolates of H. contortus. Using single worm PCR assays, we found that the presence of S168T was strongly associated with LEV resistance in the parental isolates and F3 progeny of the genetic cross surviving LEV treatment. We developed and optimised an allele-specific PCR assay for the detection of S168T and validated the assay using laboratory isolates and field samples that were phenotyped for LEV resistance. In the LEV-resistant field population, a high proportion (>75%) of L3 encoded the S168T variant, whereas the variant was absent in the susceptible isolates studied. These data further support the potential role of acr-8 S168T in LEV resistance, with the allele-specific PCR providing an important step towards establishing a sensitive molecular diagnostic test for LEV resistance.
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Affiliation(s)
- Alistair Antonopoulos
- School of Veterinary Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom; Institute of Biodiversity, Animal Health, & Comparative Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom.
| | - Stephen R. Doyle
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | | | | | | | - Sue Howell
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, USA
| | - Cedric Neveu
- Institut National de la Recherche Agronomique, Nouzilly, France
| | - Valentina Busin
- School of Veterinary Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Eileen Devaney
- Institute of Biodiversity, Animal Health, & Comparative Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Roz Laing
- Institute of Biodiversity, Animal Health, & Comparative Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom.
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Baltrušis P, Doyle SR, Halvarsson P, Höglund J. Genome-wide analysis of the response to ivermectin treatment by a Swedish field population of Haemonchus contortus. Int J Parasitol Drugs Drug Resist 2022; 18:12-19. [PMID: 34959200 PMCID: PMC8718930 DOI: 10.1016/j.ijpddr.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022]
Abstract
Haemonchus contortus is a pathogenic gastrointestinal nematode of small ruminants and, in part due to its capacity to develop resistance to drugs, contributes to significant losses in the animal production sector worldwide. Despite decades of research, comparatively little is known about the specific mechanism(s) driving resistance to drugs such as ivermectin in this species. Here we describe a genome-wide approach to detect evidence of selection by ivermectin treatment in a field population of H. contortus from Sweden, using parasites sampled from the same animals before and seven days after ivermectin exposure followed by whole-genome sequencing. Despite an 89% reduction in parasites recovered after treatment measured by the fecal egg count reduction test, the surviving population was highly genetically similar to the population before treatment, suggesting that resistance has likely evolved over time and that resistance alleles are present on diverse haplotypes. Pairwise gene and SNP frequency comparisons indicated the highest degree of differentiation was found at the terminal end of chromosome 4, whereas the most striking difference in nucleotide diversity was observed in a region on chromosome 5 previously reported to harbor a major quantitative trait locus involved in ivermectin resistance. These data provide novel insight into the genome-wide effect of ivermectin selection in a field population as well as confirm the importance of the previously established quantitative trait locus in the development of resistance to ivermectin.
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Affiliation(s)
- Paulius Baltrušis
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences, P.O. Box 7036, Uppsala, Sweden.
| | - Stephen R Doyle
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Peter Halvarsson
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences, P.O. Box 7036, Uppsala, Sweden
| | - Johan Höglund
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences, P.O. Box 7036, Uppsala, Sweden
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21
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Charlier J, Bartley DJ, Sotiraki S, Martinez-Valladares M, Claerebout E, von Samson-Himmelstjerna G, Thamsborg SM, Hoste H, Morgan ER, Rinaldi L. Anthelmintic resistance in ruminants: challenges and solutions. ADVANCES IN PARASITOLOGY 2022; 115:171-227. [PMID: 35249662 DOI: 10.1016/bs.apar.2021.12.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Anthelmintic resistance (AR) is a growing concern for effective parasite control in farmed ruminants globally. Combatting AR will require intensified and integrated research efforts in the development of innovative diagnostic tests to detect helminth infections and AR, sustainable anthelmintic treatment strategies and the development of complementary control approaches such as vaccination and plant-based control. It will also require a better understanding of socio-economic drivers of anthelmintic treatment decisions, in order to support a behavioural shift and develop targeted communication strategies that promote the uptake of evidence-based sustainable solutions. Here, we review the state-of-the-art in these different fields of research activity related to AR in helminths of livestock ruminants in Europe and beyond. We conclude that in the advent of new challenges and solutions emerging from continuing spread of AR and intensified research efforts, respectively, there is a strong need for transnational multi-actor initiatives. These should involve all key stakeholders to develop indicators of infection and sustainable control, set targets and promote good practices to achieve them.
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Affiliation(s)
| | - D J Bartley
- Disease Control, Moredun Research Institute, Penicuik, United Kingdom
| | - S Sotiraki
- Veterinary Research Institute, Hellenic Agricultural Organisation ELGO-DIMITRA, Thessaloniki, Greece
| | - M Martinez-Valladares
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Departamento de Sanidad Animal, León, Spain
| | - E Claerebout
- Ghent University, Faculty of Veterinary Medicine, Laboratory of Parasitology, Merelbeke, Belgium
| | - G von Samson-Himmelstjerna
- Institute for Parasitology and Tropical Veterinary Medicine, Veterinary Centre for Resistance Research, Freie Universität Berlin, Berlin, Germany
| | - S M Thamsborg
- Veterinary Parasitology, University of Copenhagen, Frederiksberg C, Denmark
| | - H Hoste
- INRAE, UMR 1225 IHAP INRAE/ENVT, Toulouse University, Toulouse, France
| | - E R Morgan
- Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
| | - L Rinaldi
- University of Naples Federico II, Unit of Parasitology and Parasitic Diseases, Department of Veterinary Medicine and Animal Production, CREMOPAR, Napoli, Italy.
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22
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ABC-transporter gene expression in ivermectin-susceptible and resistant Haemonchus contortus isolates. Vet Parasitol 2022; 302:109647. [DOI: 10.1016/j.vetpar.2022.109647] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/15/2021] [Accepted: 01/05/2022] [Indexed: 11/21/2022]
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23
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A journey through 50 years of research relevant to the control of gastrointestinal nematodes in ruminant livestock and thoughts on future directions. Int J Parasitol 2021; 51:1133-1151. [PMID: 34774857 DOI: 10.1016/j.ijpara.2021.10.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 11/20/2022]
Abstract
This review article provides an historical perspective on some of the major research advances of relevance to ruminant livestock gastrointestinal nematode control over the last 50 years. Over this period, gastrointestinal nematode control has been dominated by the use of broad-spectrum anthelmintic drugs. Whilst this has provided unprecedented levels of successful control for many years, this approach has been gradually breaking down for more than two decades and is increasingly unsustainable which is due, at least in part, to the emergence of anthelmintic drug resistance and a number of other factors discussed in this article. We first cover the remarkable success story of the discovery and development of broad-spectrum anthelmintic drugs, the changing face of anthelmintic drug discovery research and the emergence of anthelmintic resistance. This is followed by a review of some of the major advances in the increasingly important area of non-pharmaceutical gastrointestinal nematode control including immunology and vaccine development, epidemiological modelling and some of the alternative control strategies such as breeding for host resistance, refugia-based methods and biological control. The last 50 years have witnessed remarkable innovation and success in research aiming to improve ruminant livestock gastrointestinal nematode control, particularly given the relatively small size of the research community and limited funding. In spite of this, the growing global demand for livestock products, together with the need to maximise production efficiencies, reduce environmental impacts and safeguard animal welfare - as well as specific challenges such as anthelmintic drug resistance and climate change- mean that gastrointestinal nematode researchers will need to be as innovative in the next 50 years as in the last.
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Berger DJ, Crellen T, Lamberton PHL, Allan F, Tracey A, Noonan JD, Kabatereine NB, Tukahebwa EM, Adriko M, Holroyd N, Webster JP, Berriman M, Cotton JA. Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration. Nat Commun 2021; 12:4776. [PMID: 34362894 PMCID: PMC8346512 DOI: 10.1038/s41467-021-24958-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 07/06/2021] [Indexed: 02/07/2023] Open
Abstract
Control and elimination of the parasitic disease schistosomiasis relies on mass administration of praziquantel. Whilst these programmes reduce infection prevalence and intensity, their impact on parasite transmission and evolution is poorly understood. Here we examine the genomic impact of repeated mass drug administration on Schistosoma mansoni populations with documented reduced praziquantel efficacy. We sequenced whole-genomes of 198 S. mansoni larvae from 34 Ugandan children from regions with contrasting praziquantel exposure. Parasites infecting children from Lake Victoria, a transmission hotspot, form a diverse panmictic population. A single round of treatment did not reduce this diversity with no apparent population contraction caused by long-term praziquantel use. We find evidence of positive selection acting on members of gene families previously implicated in praziquantel action, but detect no high frequency functionally impactful variants. As efforts to eliminate schistosomiasis intensify, our study provides a foundation for genomic surveillance of this major human parasite.
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Affiliation(s)
- Duncan J Berger
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
- Department of Pathology and Pathogen Biology, Centre for Emerging, Endemic and Exotic Diseases, Royal Veterinary College, University of London, Herts, UK.
| | - Thomas Crellen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- Imperial College London, Department of Infectious Disease Epidemiology, London, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Poppy H L Lamberton
- Imperial College London, Department of Infectious Disease Epidemiology, London, UK
- Institute for Biodiversity, Animal Health, and Comparative Medicine, and Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Fiona Allan
- The Natural History Museum, Department of Life Sciences, London, UK
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jennifer D Noonan
- Institute of Parasitology, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Narcis B Kabatereine
- Vector Borne & Neglected Tropical Disease Control Division, Ministry of Health, Kampala, Uganda
| | - Edridah M Tukahebwa
- Vector Borne & Neglected Tropical Disease Control Division, Ministry of Health, Kampala, Uganda
| | - Moses Adriko
- Vector Borne & Neglected Tropical Disease Control Division, Ministry of Health, Kampala, Uganda
| | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Joanne P Webster
- Department of Pathology and Pathogen Biology, Centre for Emerging, Endemic and Exotic Diseases, Royal Veterinary College, University of London, Herts, UK.
- Imperial College London, Department of Infectious Disease Epidemiology, London, UK.
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
| | - James A Cotton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
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Sloan S, Jenvey CJ, Piedrafita D, Preston S, Stear MJ. Comparative evaluation of different molecular methods for DNA extraction from individual Teladorsagia circumcincta nematodes. BMC Biotechnol 2021; 21:35. [PMID: 34001079 PMCID: PMC8130168 DOI: 10.1186/s12896-021-00695-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background The purpose of this study was to develop a reliable DNA extraction protocol to use on individual Teladorsagia circumcincta nematode specimens to produce high quality DNA for genome sequencing and phylogenetic analysis. Pooled samples have been critical in providing the groundwork for T. circumcincta genome construction, but there is currently no standard method for extracting high-quality DNA from individual nematodes. 11 extraction kits were compared based on DNA quality, yield, and processing time. Results 11 extraction protocols were compared, and the concentration and purity of the extracted DNA was quantified. Median DNA concentration among all methods measured on NanoDrop 2000™ ranged between 0.45–11.5 ng/μL, and on Qubit™ ranged between undetectable – 0.962 ng/μL. Median A260/280 ranged between 0.505–3.925, and median A260/230 ranged − 0.005 – 1.545. Larval exsheathment to remove the nematode cuticle negatively impacted DNA concentration and purity. Conclusions A Schistosoma sp. DNA extraction method was determined as most suitable for individual T. circumcincta nematode specimens due to its resulting DNA concentration, purity, and relatively fast processing time. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00695-6.
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Affiliation(s)
- S Sloan
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia.
| | - C J Jenvey
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia
| | - D Piedrafita
- School of Science, Psychology and Sport, Federation University, Churchill, Victoria, Australia
| | - S Preston
- School of Science, Psychology and Sport, Federation University, Churchill, Victoria, Australia
| | - M J Stear
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia
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Evans KS, Wit J, Stevens L, Hahnel SR, Rodriguez B, Park G, Zamanian M, Brady SC, Chao E, Introcaso K, Tanny RE, Andersen EC. Two novel loci underlie natural differences in Caenorhabditis elegans abamectin responses. PLoS Pathog 2021; 17:e1009297. [PMID: 33720993 PMCID: PMC7993787 DOI: 10.1371/journal.ppat.1009297] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/25/2021] [Accepted: 03/02/2021] [Indexed: 11/18/2022] Open
Abstract
Parasitic nematodes cause a massive worldwide burden on human health along with a loss of livestock and agriculture productivity. Anthelmintics have been widely successful in treating parasitic nematodes. However, resistance is increasing, and little is known about the molecular and genetic causes of resistance for most of these drugs. The free-living roundworm Caenorhabditis elegans provides a tractable model to identify genes that underlie resistance. Unlike parasitic nematodes, C. elegans is easy to maintain in the laboratory, has a complete and well annotated genome, and has many genetic tools. Using a combination of wild isolates and a panel of recombinant inbred lines constructed from crosses of two genetically and phenotypically divergent strains, we identified three genomic regions on chromosome V that underlie natural differences in response to the macrocyclic lactone (ML) abamectin. One locus was identified previously and encodes an alpha subunit of a glutamate-gated chloride channel (glc-1). Here, we validate and narrow two novel loci using near-isogenic lines. Additionally, we generate a list of prioritized candidate genes identified in C. elegans and in the parasite Haemonchus contortus by comparison of ML resistance loci. These genes could represent previously unidentified resistance genes shared across nematode species and should be evaluated in the future. Our work highlights the advantages of using C. elegans as a model to better understand ML resistance in parasitic nematodes.
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Affiliation(s)
- Kathryn S. Evans
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, United States of America
| | - Janneke Wit
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Lewis Stevens
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Steffen R. Hahnel
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Briana Rodriguez
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Grace Park
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Mostafa Zamanian
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Shannon C. Brady
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, United States of America
| | - Ellen Chao
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Katherine Introcaso
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Robyn E. Tanny
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Erik C. Andersen
- Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- * E-mail:
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Gerhard AP, Krücken J, Neveu C, Charvet CL, Harmache A, von Samson-Himmelstjerna G. Pharyngeal Pumping and Tissue-Specific Transgenic P-Glycoprotein Expression Influence Macrocyclic Lactone Susceptibility in Caenorhabditis elegans. Pharmaceuticals (Basel) 2021; 14:153. [PMID: 33668460 PMCID: PMC7917992 DOI: 10.3390/ph14020153] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 11/16/2022] Open
Abstract
Macrocyclic lactones (MLs) are widely used drugs to treat and prevent parasitic nematode infections. In many nematode species including a major pathogen of foals, Parascaris univalens, resistance against MLs is widespread, but the underlying resistance mechanisms and ML penetration routes into nematodes remain unknown. Here, we examined how the P-glycoprotein efflux pumps, candidate genes for ML resistance, can modulate drug susceptibility and investigated the role of active drug ingestion for ML susceptibility in the model nematode Caenorhabditis elegans. Wildtype or transgenic worms, modified to overexpress P. univalens PGP-9 (Pun-PGP-9) at the intestine or epidermis, were incubated with ivermectin or moxidectin in the presence (bacteria or serotonin) or absence (no specific stimulus) of pharyngeal pumping (PP). Active drug ingestion by PP was identified as an important factor for ivermectin susceptibility, while moxidectin susceptibility was only moderately affected. Intestinal Pun-PGP-9 expression elicited a protective effect against ivermectin and moxidectin only in the presence of PP stimulation. Conversely, epidermal Pun-PGP-9 expression protected against moxidectin regardless of PP and against ivermectin only in the absence of active drug ingestion. Our results demonstrate the role of active drug ingestion by nematodes for susceptibility and provide functional evidence for the contribution of P-glycoproteins to ML resistance in a tissue-specific manner.
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Affiliation(s)
- Alexander P. Gerhard
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany; (A.P.G.); (J.K.)
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany; (A.P.G.); (J.K.)
| | - Cedric Neveu
- INRAE, Université de Tours, ISP, F-37380 Nouzilly, France; (C.N.); (C.L.C.); (A.H.)
| | - Claude L. Charvet
- INRAE, Université de Tours, ISP, F-37380 Nouzilly, France; (C.N.); (C.L.C.); (A.H.)
| | - Abdallah Harmache
- INRAE, Université de Tours, ISP, F-37380 Nouzilly, France; (C.N.); (C.L.C.); (A.H.)
| | - Georg von Samson-Himmelstjerna
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany; (A.P.G.); (J.K.)
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Mohammedsalih KM, Krücken J, Bashar A, Juma FR, Abdalmalaik AAH, Khalafalla A, Abakar A, Coles G, von Samson-Himmelstjerna G. Susceptible trichostrongyloid species mask presence of benzimidazole-resistant Haemonchus contortus in cattle. Parasit Vectors 2021; 14:101. [PMID: 33557939 PMCID: PMC7869217 DOI: 10.1186/s13071-021-04593-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/11/2021] [Indexed: 11/25/2022] Open
Abstract
Background Benzimidazole (BZ) anthelmintics are widely used to control infections with parasitic nematodes, but BZ resistance is an emerging threat among several nematode species infecting humans and animals. In Sudan, BZ-resistant Haemonchus contortus populations were recently reported in goats in South Darfur State. The objective of this study was to collect data regarding the situation of BZ resistance in cattle parasitic nematodes in South Darfur using phenotypic and molecular approaches, besides providing some epidemiological data on nematodes in cattle. Methods The faecal egg count reduction test and the egg hatch test (EHT) were used to evaluate benzimidazole efficacy in cattle nematodes in five South Darfur study areas: Beleil, Kass, Nyala, Rehed Al-Birdi and Tulus. Genomic DNA was extracted from pools of third-stage larvae (L3) (n = 40) during trials, before and after treatment, and pools of adult male Haemonchus spp. (n = 18) from abattoirs. The polymorphisms F167Y, E198A and F200Y in isotype 1 β-tubulin genes of H. contortus and H. placei were analysed using Sanger and pyrosequencing. Results Prevalence of gastro-intestinal helminths in cattle was 71% (313/443). Reduced albendazole faecal egg count reduction efficacy was detected in three study areas: Nyala (93.7%), Rehed Al-Birdi (89.7%) and Tulus (88.2%). In the EHT, EC50 values of these study areas ranged between 0.032 and 0.037 µg/ml thiabendazole. Genus-specific PCRs detected the genera Haemonchus, Trichostrongylus and Cooperia in L3 samples collected after albendazole treatment. Sanger sequencing followed by pyrosequencing assays did not detect elevated frequencies of known BZ resistance-associated alleles in codon F167Y, E198A and F200Y in isotype 1 β-tubulin gene of H. placei (≤ 11.38%). However, polymorphisms were detected in H. contortus and in samples with mixed infections with H. contortus and H. placei at codon 198, including E198L (16/58), E198V (2/58) and potentially E198Stop (1/58). All pooled L3 samples post-albendazole treatment (n = 13) were identified as H. contortus with an E198L substitution at codon 198. Conclusions To the knowledge of the authors, this is the first report of reduced albendazole efficacy in cattle in Sudan and is the first study describing an E198L substitution in phenotypically BZ-resistant nematodes collected from cattle.![]()
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Affiliation(s)
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Street 7-13, 14163, Berlin, Germany
| | - Ahmed Bashar
- Faculty of Veterinary Science, University of Nyala, P.O. Box 155, Nyala, Sudan
| | - Fathel-Rahman Juma
- Faculty of Veterinary Science, University of Nyala, P.O. Box 155, Nyala, Sudan
| | | | - Amna Khalafalla
- Faculty of Veterinary Medicine, University of Khartoum, P.O. Box 32, Khartoum North, Sudan
| | - Adam Abakar
- Faculty of Medical Laboratory Sciences, University of Gezira, P.O. Box 20, Wadmedani, Sudan
| | - Gerald Coles
- Ubley Biologics, Ubley, P.O. Box 170, Bristol, BS40 6JA, UK
| | - Georg von Samson-Himmelstjerna
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Street 7-13, 14163, Berlin, Germany.
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Kotze AC, Gilleard JS, Doyle SR, Prichard RK. Challenges and opportunities for the adoption of molecular diagnostics for anthelmintic resistance. Int J Parasitol Drugs Drug Resist 2020; 14:264-273. [PMID: 33307336 PMCID: PMC7726450 DOI: 10.1016/j.ijpddr.2020.11.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/22/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023]
Abstract
Anthelmintic resistance is a significant threat to livestock production systems worldwide and is emerging as an important issue in companion animal parasite management. It is also an emerging concern for the control of human soil-transmitted helminths and filaria. An important aspect of managing anthelmintic resistance is the ability to utilise diagnostic tests to detect its emergence at an early stage. In host-parasite systems where resistance is already widespread, diagnostics have a potentially important role in determining those drugs that remain the most effective. The development of molecular diagnostics for anthelmintic resistance is one focus of the Consortium for Anthelmintic Resistance and Susceptibility (CARS) group. The present paper reflects discussions of this issue that occurred at the most recent meeting of the group in Wisconsin, USA, in July 2019. We compare molecular resistance diagnostics with in vivo and in vitro phenotypic methods, and highlight the advantages and disadvantages of each. We assess whether our knowledge on the identity of molecular markers for resistance towards the different drug classes is sufficient to provide some expectation that molecular tests for field use may be available in the short-to-medium term. We describe some practical aspects of such tests and how our current capabilities compare to the requirements of an 'ideal' test. Finally, we describe examples of drug class/parasite species interactions that provide the best opportunity for commercial use of molecular tests in the near future. We argue that while such prototype tests may not satisfy the requirements of an 'ideal' test, their potential to provide significant advances over currently-used phenotypic methods warrants their development as field diagnostics.
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Affiliation(s)
- Andrew C. Kotze
- CSIRO Agriculture and Food, St. Lucia, Brisbane, 4072, QLD, Australia,Corresponding author. , CSIRO Agriculture and Food, St. Lucia, Brisbane, 4072, QLD, Australia.
| | - John S. Gilleard
- Department of Comparative Biology and Experimental Medicine, Host-Parasite Interactions Program, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Stephen R. Doyle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Roger K. Prichard
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, QC, H9X 3V9, Canada
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Ivermectin: An Anthelmintic, an Insecticide, and Much More. Trends Parasitol 2020; 37:48-64. [PMID: 33189582 DOI: 10.1016/j.pt.2020.10.005] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/26/2022]
Abstract
Here we tell the story of ivermectin, describing its anthelmintic and insecticidal actions and recent studies that have sought to reposition ivermectin for the treatment of other diseases that are not caused by helminth and insect parasites. The standard theory of its anthelmintic and insecticidal mode of action is that it is a selective positive allosteric modulator of glutamate-gated chloride channels found in nematodes and insects. At higher concentrations, ivermectin also acts as an allosteric modulator of ion channels found in host central nervous systems. In addition, in tissue culture, at concentrations higher than anthelmintic concentrations, ivermectin shows antiviral, antimalarial, antimetabolic, and anticancer effects. Caution is required before extrapolating from these preliminary repositioning experiments to clinical use, particularly for Covid-19 treatment, because of the high concentrations of ivermectin used in tissue-culture experiments.
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Palevich N, Maclean PH, Choi YJ, Mitreva M. Characterization of the Complete Mitochondrial Genomes of Two Sibling Species of Parasitic Roundworms, Haemonchus contortus and Teladorsagia circumcincta. Front Genet 2020; 11:573395. [PMID: 33133162 PMCID: PMC7578395 DOI: 10.3389/fgene.2020.573395] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/18/2020] [Indexed: 12/20/2022] Open
Abstract
Haemonchus contortus and Teladorsagia circumcincta are among the two most pathogenic internal parasitic nematodes infecting small ruminants, such as sheep and goats, and are a global animal health issue. Accurate identification and delineation of Haemonchidae species is essential for development of diagnostic and control strategies with high resolution for Trichostrongyloidea infection in ruminants. Here, we describe in detail and compare the complete mitochondrial (mt) genomes of the New Zealand H. contortus and T. circumcincta field strains to improve our understanding of species- and strain-level evolution in these closely related roundworms. In the present study, we performed extensive comparative bioinformatics analyses on the recently sequenced complete mt genomes of the New Zealand H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP field strains. Amino acid sequences inferred from individual genes of each of the two mt genomes were compared, concatenated and subjected to phylogenetic analysis using Bayesian inference (BI), Maximum Likelihood (ML), and Maximum Parsimony (MP). The AT-rich mt genomes of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP are 14,001 bp (A+T content of 77.4%) and 14,081 bp (A+T content of 77.3%) in size, respectively. All 36 of the typical nematode mt genes are transcribed in the forward direction in both species and comprise of 12 protein-encoding genes (PCGs), 2 ribosomal RNA (rrn) genes, and 22 transfer RNA (trn) genes. The secondary structures for the 22 trn genes and two rrn genes differ between H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP, however the gene arrangements of both are consistent with other Trichostrongylidea sequenced to date. Comparative analyses of the complete mitochondrial nucleotide sequences, PCGs, A+T rich and non-coding repeat regions of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP further reinforces the high levels of diversity and gene flow observed among Trichostrongylidea, and supports their potential as ideal markers for strain-level identification from different hosts and geographical regions with high resolution for future studies. The complete mt genomes of H. contortus NZ_Hco_NP and T. circumcincta NZ_Teci_NP presented here provide useful novel markers for further studies of the meta-population connectivity and the genetic mechanisms driving evolution in nematode species.
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Affiliation(s)
- Nikola Palevich
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Paul H. Maclean
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Young-Jun Choi
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Makedonka Mitreva
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
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Martínez-Valladares M, Valderas-García E, Gandasegui J, Skuce P, Morrison A, Castilla Gómez de Agüero V, Cambra-Pellejà M, Balaña-Fouce R, Rojo-Vázquez FA. Teladorsagia circumcincta beta tubulin: the presence of the E198L polymorphism on its own is associated with benzimidazole resistance. Parasit Vectors 2020; 13:453. [PMID: 32894163 PMCID: PMC7487696 DOI: 10.1186/s13071-020-04320-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/30/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Benzimidazole resistance is associated with isotype-1 β-tubulin gene F200Y, E198A and F167Y SNPs. In this study, the recently described polymorphism E198L was reported and analysed in Teladorsagia circumcincta. METHODS The benzimidazole phenotypic resistance was measured by the faecal egg count reduction test (FECRT) and the egg hatch test (EHT) using a discriminating dose (DD) in 39 sheep flocks. Around 1000 larvae collected before and after treatment were used for DNA extraction. The resistant species identified in all flocks was T. circumcincta. The resistance alleles frequencies were measured for F200Y and E198A. A 371-bp fragment of the isotype-1 β-tubulin gene was analysed, including the three codons of interest, and a new pyrosequencing assay was designed for testing E198L. RESULTS The percentage of resistant flocks was 35% by FECRT or 26% by EHT; however, F200Y and E198A SNPs were absent in T. circumcincta. The amplification of a 371-bp fragment confirmed the absence of F167Y and F200Y in 6 resistant flocks. Regarding codon 198, all samples after treatment carried a leucine (CTA). A pyrosequencing assay analysed the allele frequencies for the first two bases at codon 198 independently, G/C and A/T. The correlation between C and T frequencies was almost 1 (r = 0.929, P < 0.0001) and the mean value of both was calculated to measure the leucine frequency; this value ranged between 10.4-80.7% before treatment, and 82.3-92.8% after treatment. High and similar correlations were reported between the genotypic variables (C frequency, T frequency or mean of both frequencies) and phenotypic resistance (r > 0.720, P < 0.0001), although negatively associated with the FECRT and positively with the EHT. According to multivariate linear regression analysis, the T frequency was the most significant variable influencing the phenotypic resistance (FECRT or EHT; P < 0.0001). In the EHT, 67.1% of the phenotypic variability is associated with the T frequency but in the FECRT only 33.4%; therefore, the EHT using a DD seems to detect the genotypic resistance more accurately than the FECRT. CONCLUSIONS The E198L polymorphism can confer BZ resistance on its own in T. circumcincta.
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Affiliation(s)
- María Martínez-Valladares
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Grulleros, 24346, León, Spain. .,Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, 24071, León, Spain.
| | - Elora Valderas-García
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Grulleros, 24346, León, Spain.,Departmento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, 24071, León, Spain
| | | | - Philip Skuce
- Moredun Research Institute, Pentlands Science Park, Edinburgh, EH26 0PZ, UK
| | - Alison Morrison
- Moredun Research Institute, Pentlands Science Park, Edinburgh, EH26 0PZ, UK
| | - Verónica Castilla Gómez de Agüero
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Grulleros, 24346, León, Spain.,Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, 24071, León, Spain
| | - Maria Cambra-Pellejà
- Instituto de Ganadería de Montaña (CSIC-Universidad de León), Grulleros, 24346, León, Spain.,Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, 24071, León, Spain
| | - Rafael Balaña-Fouce
- Departmento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, 24071, León, Spain
| | - Francisco A Rojo-Vázquez
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana, 24071, León, Spain
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Gerhard AP, Krücken J, Heitlinger E, Janssen IJI, Basiaga M, Kornaś S, Beier C, Nielsen MK, Davis RE, Wang J, von Samson-Himmelstjerna G. The P-glycoprotein repertoire of the equine parasitic nematode Parascaris univalens. Sci Rep 2020; 10:13586. [PMID: 32788636 PMCID: PMC7423980 DOI: 10.1038/s41598-020-70529-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/21/2020] [Indexed: 12/20/2022] Open
Abstract
P-glycoproteins (Pgp) have been proposed as contributors to the widespread macrocyclic lactone (ML) resistance in several nematode species including a major pathogen of foals, Parascaris univalens. Using new and available RNA-seq data, ten different genomic loci encoding Pgps were identified and characterized by transcriptome-guided RT-PCRs and Sanger sequencing. Phylogenetic analysis revealed an ascarid-specific Pgp lineage, Pgp-18, as well as two paralogues of Pgp-11 and Pgp-16. Comparative gene expression analyses in P. univalens and Caenorhabditis elegans show that the intestine is the major site of expression but individual gene expression patterns were not conserved between the two nematodes. In P. univalens, PunPgp-9, PunPgp-11.1 and PunPgp-16.2 consistently exhibited the highest expression level in two independent transcriptome data sets. Using RNA-Seq, no significant upregulation of any Pgp was detected following in vitro incubation of adult P. univalens with ivermectin suggesting that drug-induced upregulation is not the mechanism of Pgp-mediated ML resistance. Expression and functional analyses of PunPgp-2 and PunPgp-9 in Saccharomyces cerevisiae provide evidence for an interaction with ketoconazole and ivermectin, but not thiabendazole. Overall, this study established reliable reference gene models with significantly improved annotation for the P. univalens Pgp repertoire and provides a foundation for a better understanding of Pgp-mediated anthelmintic resistance.
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Affiliation(s)
- Alexander P Gerhard
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Emanuel Heitlinger
- Institute of Biology, Molecular Parasitology, Humboldt-Universität Zu Berlin, Berlin, Germany.,Leibniz Institute for Zoo and Wildlife Research, Research Group Ecology and Evolution of Parasite Host Interactions, Berlin, Germany
| | - I Jana I Janssen
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Marta Basiaga
- Department of Zoology and Animal Welfare, University of Agriculture in Kraków, Kraków, Poland
| | - Sławomir Kornaś
- Department of Zoology and Animal Welfare, University of Agriculture in Kraków, Kraków, Poland
| | - Céline Beier
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Martin K Nielsen
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, USA
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, USA
| | - Jianbin Wang
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
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Mohammedsalih KM, Krücken J, Khalafalla A, Bashar A, Juma FR, Abakar A, Abdalmalaik AAH, Coles G, von Samson-Himmelstjerna G. New codon 198 β-tubulin polymorphisms in highly benzimidazole resistant Haemonchus contortus from goats in three different states in Sudan. Parasit Vectors 2020; 13:114. [PMID: 32122383 PMCID: PMC7053126 DOI: 10.1186/s13071-020-3978-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/17/2020] [Indexed: 01/12/2023] Open
Abstract
Background Benzimidazole (BZ) resistance in gastrointestinal nematodes is a worldwide problem for livestock production, particularly in small ruminants. Assignment of the emergence of resistance using sensitive and reliable methods is required to adopt the correct strategies for control. In Sudan, BZ resistant Haemonchus contortus populations were recently reported in goats in South Darfur. This study aimed to provide additional data regarding albendazole efficacy and to describe the prevailing molecular BZ resistance mechanisms. Methods Faecal egg count reduction and egg hatch tests (EHT) were used to evaluate albendazole efficacy in three different areas of South Darfur using naturally (Rehed Al-Birdi and Tulus) and experimentally infected (Tulus and Um Dafuq) goats. Using samples from Central, East and South Darfur, pyro- and Sanger sequencing were used to detect the polymorphisms F167Y, E198A and F200Y in H. contortus isotype 1 β-tubulin in DNA extracted from pooled third-stage larval (L3) samples (n = 36) on days 0 and 10 during trials, and from pooled adult male H. contortus (treated goats, n = 14; abattoirs, n = 83) including samples from populations previously found to be resistant in South Darfur. Results Albendazole efficacies at 5, 7.5 and 10 mg/kg doses were 73.5–90.2% on day 14 in natural and experimental infections while 12.5 mg/kg showed > 96.6% efficacy. EC50 in the EHT were 0.8 and 0.11 µg/ml thiabendazole in natural and experimental infection trials, respectively. PCRs detected Haemonchus, Trichostrongylus and Cooperia in L3 samples from albendazole-treated goats. Haemonchus contortus allele frequencies in codons 167 and 200 using pyrosequencing assays were ≤ 7.4% while codon 198 assays failed. Sanger sequencing revealed five novel polymorphisms at codon 198. Noteworthy, an E198L substitution was present in 82% of the samples (L3 and adults) including all post-treatment samples. Moreover, E198V, E198K and potentially E198I, and E198Stop were identified in a few samples. Conclusions To our knowledge, this is the first report of E198L in BZ resistant H. contortus and the second where this is the predominant genotype associated with resistance in any strongyle species. Since this variant cannot be quantified using pyrosequencing, the results highlight important limitations in the general applicability of pyrosequencing to quantify BZ resistance genotypes.![]()
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Affiliation(s)
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany
| | - Amna Khalafalla
- Faculty of Veterinary Medicine, University of Khartoum, PO Box 32, Khartoum North, Sudan
| | - Ahmed Bashar
- Faculty of Veterinary Science, University of Nyala, Nyala, Sudan
| | | | - Adam Abakar
- Faculty of Medical Laboratory Sciences, University of Gezira, PO Box 20, Wad Medani, Sudan
| | | | - Gerald Coles
- Ubley Biologics, PO Box 170, Ubley, Bristol, BS40 6JA, UK
| | - Georg von Samson-Himmelstjerna
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany
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Hedtke SM, Kuesel AC, Crawford KE, Graves PM, Boussinesq M, Lau CL, Boakye DA, Grant WN. Genomic Epidemiology in Filarial Nematodes: Transforming the Basis for Elimination Program Decisions. Front Genet 2020; 10:1282. [PMID: 31998356 PMCID: PMC6964045 DOI: 10.3389/fgene.2019.01282] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/21/2019] [Indexed: 11/25/2022] Open
Abstract
Onchocerciasis and lymphatic filariasis are targeted for elimination, primarily using mass drug administration at the country and community levels. Elimination of transmission is the onchocerciasis target and global elimination as a public health problem is the end point for lymphatic filariasis. Where program duration, treatment coverage, and compliance are sufficiently high, elimination is achievable for both parasites within defined geographic areas. However, transmission has re-emerged after apparent elimination in some areas, and in others has continued despite years of mass drug treatment. A critical question is whether this re-emergence and/or persistence of transmission is due to persistence of local parasites-i.e., the result of insufficient duration or drug coverage, poor parasite response to the drugs, or inadequate methods of assessment and/or criteria for determining when to stop treatment-or due to re-introduction of parasites via human or vector movement from another endemic area. We review recent genetics-based research exploring these questions in Onchocerca volvulus, the filarial nematode that causes onchocerciasis, and Wuchereria bancrofti, the major pathogen for lymphatic filariasis. We focus in particular on the combination of genomic epidemiology and genome-wide associations to delineate transmission zones and distinguish between local and introduced parasites as the source of resurgence or continuing transmission, and to identify genetic markers associated with parasite response to chemotherapy. Our ultimate goal is to assist elimination efforts by developing easy-to-use tools that incorporate genetic information about transmission and drug response for more effective mass drug distribution, surveillance strategies, and decisions on when to stop interventions to improve sustainability of elimination.
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Affiliation(s)
- Shannon M. Hedtke
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Annette C. Kuesel
- Unicef/UNDP/World Bank/World Health Organization Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Katie E. Crawford
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Patricia M. Graves
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, QLD, Australia
| | - Michel Boussinesq
- Unité Mixte Internationale 233 "TransVIHMI", Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Colleen L. Lau
- Department of Global Health, Research School of Population Health, Australian National University, Acton, ACT, Australia
| | - Daniel A. Boakye
- Parasitology Department, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - Warwick N. Grant
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
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Fauver JR, Martin J, Weil GJ, Mitreva M, Fischer PU. De novo Assembly of the Brugia malayi Genome Using Long Reads from a Single MinION Flowcell. Sci Rep 2019; 9:19521. [PMID: 31863009 PMCID: PMC6925183 DOI: 10.1038/s41598-019-55908-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/28/2019] [Indexed: 11/15/2022] Open
Abstract
Filarial nematode infections cause a substantial global disease burden. Genomic studies of filarial worms can improve our understanding of their biology and epidemiology. However, genomic information from field isolates is limited and available reference genomes are often discontinuous. Single molecule sequencing technologies can reduce the cost of genome sequencing and long reads produced from these devices can improve the contiguity and completeness of genome assemblies. In addition, these new technologies can make generation and analysis of large numbers of field isolates feasible. In this study, we assessed the performance of the Oxford Nanopore Technologies MinION for sequencing and assembling the genome of Brugia malayi, a human parasite widely used in filariasis research. Using data from a single MinION flowcell, a 90.3 Mb nuclear genome was assembled into 202 contigs with an N50 of 2.4 Mb. This assembly covered 96.9% of the well-defined B. malayi reference genome with 99.2% identity. The complete mitochondrial genome was obtained with individual reads and the nearly complete genome of the endosymbiotic bacteria Wolbachia was assembled alongside the nuclear genome. Long-read data from the MinION produced an assembly that approached the quality of a well-established reference genome using comparably fewer resources.
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Affiliation(s)
- Joseph R Fauver
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States.
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States.
| | - John Martin
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
| | - Gary J Weil
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, United States
| | - Peter U Fischer
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
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Turnbull F, Devaney E, Morrison AA, Laing R, Bartley DJ. Genotypic characterisation of monepantel resistance in historical and newly derived field strains of Teladorsagia circumcincta. Int J Parasitol Drugs Drug Resist 2019; 11:59-69. [PMID: 31622822 PMCID: PMC6796645 DOI: 10.1016/j.ijpddr.2019.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 11/24/2022]
Abstract
Recent reports of monepantel (MPTL) resistance in UK field isolates of Teladorsagia circumcincta has highlighted the need for a better understanding of the mechanism of MPTL-resistance in order to preserve its anthelmintic efficacy in this economically important species. Nine discrete populations of T. circumcincta were genotypically characterised; three MPTL-susceptible isolates, three experimentally selected MPTL-resistant strains and three field derived populations. Full-length Tci-mptl-1 gene sequences were generated and comparisons between the MPTL-susceptible isolates, MPTL-resistant strains and one field isolate, showed that different putative MPTL-resistance conferring mutations were present in different resistant isolates. Truncated forms of the Tci-mptl-1 gene were also observed. The genetic variability of individual larvae, within and between populations, was examined using microsatellite analyses at 10 'neutral' loci (presumed to be unaffected by MPTL). Results confirmed that there was little background genetic variation between the populations, global FST <0.038. Polymorphisms present in exons 7 and 8 of Tci-mptl-1 enabled genotyping of individual larvae. A reduction in the number of genotypes was observed in all MPTL-resistant strains compared to the MPTL-susceptible strains that they were derived from, suggesting there was purifying selection at Tci-mptl-1 as a result of MPTL-treatment. The potential link between benzimidazole (BZ)-resistance and MPTL-resistance was examined by screening individual larvae for the presence of three SNPs associated with BZ-resistance in the β-tubulin isotype-1 gene. The majority of larvae were BZ-susceptible homozygotes at positions 167 and 198. Increased heterozygosity at position 200 was observed in the MPTL-resistant strains compared to their respective MPTL-susceptible population. There was no decrease in the occurrence of BZ-resistant genotypes in larvae from each population. These differences, in light of the purifying selection at this locus in all MPTL-resistant isolates, suggests that Tci-mptl-1 confers MPTL-resistance in T. circumcincta, as in Haemonchus contortus, but that different mutations in Tci-mptl-1 can confer resistance in different populations.
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Affiliation(s)
- Frank Turnbull
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, United Kingdom; Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, EH26 0PZ, United Kingdom.
| | - Eileen Devaney
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, United Kingdom
| | - Alison A Morrison
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, EH26 0PZ, United Kingdom
| | - Roz Laing
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, United Kingdom
| | - Dave J Bartley
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, EH26 0PZ, United Kingdom
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Palevich N, Maclean PH, Mitreva M, Scott R, Leathwick D. The complete mitochondrial genome of the New Zealand parasitic roundworm Teladorsagia circumcincta (Trichostrongyloidea: Haemonchidae) field strain NZ_Teci_NP. Mitochondrial DNA B Resour 2019; 4:2869-2871. [PMID: 33365767 PMCID: PMC7706463 DOI: 10.1080/23802359.2019.1660241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 07/31/2019] [Indexed: 11/20/2022] Open
Abstract
The complete mitochondrial genome of the New Zealand parasitic nematode Teladorsagia circumcincta field strain NZ_Teci_NP was sequenced and annotated. The 14,083 bp-long mitogenome contains 12 protein-coding genes (atp8 gene missing), two ribosomal RNAs (rRNAs), and 22 transfer RNAs (tRNAs). Phylogenetic analysis showed that T. circumcincta NZ_Teci_NP forms a monophyletic cluster with the remaining Haemonchidae species and further reinforces the high levels of diversity and gene flow observed among Trichostrongylidae.
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Affiliation(s)
- Nikola Palevich
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Paul H. Maclean
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Makedonka Mitreva
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Richard Scott
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - David Leathwick
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
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Extreme-QTL mapping of monepantel resistance in Haemonchus contortus. Parasit Vectors 2019; 12:403. [PMID: 31412938 PMCID: PMC6693152 DOI: 10.1186/s13071-019-3663-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/09/2019] [Indexed: 11/25/2022] Open
Abstract
Background Haemonchus contortus, a gastrointestinal nematode parasite of sheep, is mainly controlled by anthelmintics; the occurrence of anthelmintic resistance leads to treatment failures and increases economic burden. Because molecular mechanisms involved in drug resistance can be elucidated by genomic studies, an extreme quantitative trait locus (X-QTL) mapping approach was used to identify co-segregation of the resistance phenotype with genetic markers to detect the genome-wide variants associated with monepantel resistance in H. contortus. Methods A cross between H. contortus isolates using parental susceptible (Par-S) males and monepantel resistant (Par-R) females resulted in SR progeny, while reciprocal cross resulted in RS progeny. Pools (n = 30,000) of infective larvae (L3) recovered from Par-R, and from SR and RS populations in the F3 generation, collected both before (unselected group) and 7 days after (selected group) selection with monepantel treatment in sheep hosts, were subjected to genome sequencing (Pool-Seq). Pairwise comparisons of allele frequencies between unselected and selected groups were performed for each population by Fisher’s exact test (FET) and for both populations combined by a Cochran-Mantel-Haenszel (CMH) test. Results Mapping rates varied from 80.29 to 81.77% at a 90.4X mean coverage of aligned reads. After correction for multiple testing, significant (P < 0.05) changes in allele frequencies were detected by FET for 6 and 57 single nucleotide polymorphisms (SNPs) in the SR and RS populations, respectively, and by the CMH test for 124 SNPs in both populations. The significant variants located on chromosome 2 generated a selection signal in a genomic region harboring the mptl-1, deg-3 and des-2 genes, previously reported as candidates for monepantel resistance. In addition, three new variants were identified in the mptl-1 gene. Conclusions This study expands knowledge on genome-wide molecular events underlying H. contortus resistance to monepantel. The identification of a genome region harboring major genes previously associated with monepantel resistance supports the results of the employed X-QTL approach. In addition, a deletion in exon 11 of the mptl-1 gene should be further investigated as the putative causal mutation leading to monepantel resistance. Electronic supplementary material The online version of this article (10.1186/s13071-019-3663-9) contains supplementary material, which is available to authorized users.
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Prichard RK, Geary TG. Perspectives on the utility of moxidectin for the control of parasitic nematodes in the face of developing anthelmintic resistance. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2019; 10:69-83. [PMID: 31229910 PMCID: PMC6593148 DOI: 10.1016/j.ijpddr.2019.06.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/12/2019] [Accepted: 06/12/2019] [Indexed: 12/22/2022]
Abstract
Macrocyclic lactone (ML) anthelmintics are the most important class of anthelmintics because of our high dependence on them for the control of nematode parasites and some ectoparasites in livestock, companion animals and in humans. However, resistance to MLs is of increasing concern. Resistance is commonplace throughout the world in nematode parasites of small ruminants and is of increasing concern in horses, cattle, dogs and other animals. It is suspected in Onchocerca volvulus in humans. In most animals, resistance first arose to the avermectins, such as ivermectin (IVM), and subsequently to moxidectin (MOX). Usually when parasite populations are ML-resistant, MOX is more effective than avermectins. MOX may have higher intrinsic potency against some parasites, especially filarial nematodes, than the avermectins. However, it clearly has a significantly different pharmacokinetic profile. It is highly distributed to lipid tissues, less likely to be removed by ABC efflux transporters, is poorly metabolized and has a long half-life. This results in effective concentrations persisting for longer in target hosts. It also has a high safety index. Limited data suggest that anthelmintic resistance may be overcome, at least temporarily, if a high concentration can be maintained at the site of the parasites for a prolonged period of time. Because of the properties of MOX, there are reasonable prospects that strains of parasites that are resistant to avermectins at currently recommended doses will be controlled by MOX if it can be administered at sufficiently high doses and in formulations that enhance its persistence in the host. This review examines the properties of MOX that support this contention and compares them with the properties of other MLs. The case for using MOX to better control ML-resistant parasites is summarised and some outstanding research questions are presented.
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Affiliation(s)
- Roger K Prichard
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, Quebec, Canada, H9X3V9.
| | - Timothy G Geary
- Institute of Parasitology, McGill University, Sainte Anne-de-Bellevue, Quebec, Canada, H9X3V9.
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Minimal modulation of macrocyclic lactone susceptibility in Caenorhabditis elegans following inhibition of cytochrome P450 monooxygenase activity. Exp Parasitol 2019; 200:61-66. [PMID: 30946841 DOI: 10.1016/j.exppara.2019.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 03/21/2019] [Accepted: 03/30/2019] [Indexed: 11/24/2022]
Abstract
Anthelmintic and in particular macrocyclic lactone (ML) resistance is a widespread problem in trichostrongyloid parasitic nematodes, yet mechanisms of ML resistance are still poorly understood. In the absence of target-site changes in resistant parasite field populations, increased drug extrusion and xenobiotic metabolism have been implicated in modification of susceptibility to MLs. In addition to P-glycoproteins, cytochrome P450 monooxygenases (CYPs) were considered to be involved in ML resistance. CYPs are highly divergent in nematodes with about 80 genes in the model organism Caenorhabditis elegans. Using larval development assays in the C. elegans model, piperonyl butoxide (PBO) and a temperature-sensitive variant of the emb-8 cytochrome reductase were used for chemical and genetic ablation of CYP activity. Additionally, a loss-of-function variant of cyp-14A5 was characterized to determine whether increased expression of this CYP in an ivermectin (IVM)-tolerant C. elegans line might be related to the phenotype. In a preliminary experiment with PBO, susceptibility to 5 nM IVM was synergistically increased by PBO. However, effects of genetic ablation of CYP activity on the EC50 values were small (1.5-fold decrease) for IVM and not significant for moxidectin (MOX). However, due to the steep concentration-response-curves, there were again strong differences between the wild-type and the CYP deficient genotype at individual IVM but not MOX concentrations. Although these results suggest small but significant effects on the susceptibility level of C. elegans to IVM, the cyp14A5 gene proposed by a previous study as candidate was ruled out since it was neither IVM/MOX inducible nor did a strain with a loss-of-function allele show increased susceptibility to either drug. In conclusion, the effect of the CYP system on IVM susceptibility in C. elegans is at best low while effects on MOX susceptibility were not detected. The previously suggested candidate cyp14A5 could be excluded to be involved in ML metabolism.
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42
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Genome-wide Approaches to Investigate Anthelmintic Resistance. Trends Parasitol 2019; 35:289-301. [DOI: 10.1016/j.pt.2019.01.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 01/09/2023]
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Doyle SR, Illingworth CJR, Laing R, Bartley DJ, Redman E, Martinelli A, Holroyd N, Morrison AA, Rezansoff A, Tracey A, Devaney E, Berriman M, Sargison N, Cotton JA, Gilleard JS. Population genomic and evolutionary modelling analyses reveal a single major QTL for ivermectin drug resistance in the pathogenic nematode, Haemonchus contortus. BMC Genomics 2019; 20:218. [PMID: 30876405 PMCID: PMC6420744 DOI: 10.1186/s12864-019-5592-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Infections with helminths cause an enormous disease burden in billions of animals and plants worldwide. Large scale use of anthelmintics has driven the evolution of resistance in a number of species that infect livestock and companion animals, and there are growing concerns regarding the reduced efficacy in some human-infective helminths. Understanding the mechanisms by which resistance evolves is the focus of increasing interest; robust genetic analysis of helminths is challenging, and although many candidate genes have been proposed, the genetic basis of resistance remains poorly resolved. RESULTS Here, we present a genome-wide analysis of two genetic crosses between ivermectin resistant and sensitive isolates of the parasitic nematode Haemonchus contortus, an economically important gastrointestinal parasite of small ruminants and a model for anthelmintic research. Whole genome sequencing of parental populations, and key stages throughout the crosses, identified extensive genomic diversity that differentiates populations, but after backcrossing and selection, a single genomic quantitative trait locus (QTL) localised on chromosome V was revealed to be associated with ivermectin resistance. This QTL was common between the two geographically and genetically divergent resistant populations and did not include any leading candidate genes, suggestive of a previously uncharacterised mechanism and/or driver of resistance. Despite limited resolution due to low recombination in this region, population genetic analyses and novel evolutionary models supported strong selection at this QTL, driven by at least partial dominance of the resistant allele, and that large resistance-associated haplotype blocks were enriched in response to selection. CONCLUSIONS We have described the genetic architecture and mode of ivermectin selection, revealing a major genomic locus associated with ivermectin resistance, the most conclusive evidence to date in any parasitic nematode. This study highlights a novel genome-wide approach to the analysis of a genetic cross in non-model organisms with extreme genetic diversity, and the importance of a high-quality reference genome in interpreting the signals of selection so identified.
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Affiliation(s)
| | - Christopher J. R. Illingworth
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH UK
- Department of Applied Maths and Theoretical Physics, Wilberforce Road, Cambridge, CB3 0WA UK
| | - Roz Laing
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Campus, Glasgow, G61 1QH UK
| | - David J. Bartley
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 0PZ UK
| | - Elizabeth Redman
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta Canada
| | - Axel Martinelli
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA UK
- Present Address: Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
- Present Address: Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nancy Holroyd
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA UK
| | - Alison A. Morrison
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, EH26 0PZ UK
| | - Andrew Rezansoff
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta Canada
| | - Alan Tracey
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA UK
| | - Eileen Devaney
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Garscube Campus, Glasgow, G61 1QH UK
| | | | - Neil Sargison
- University of Edinburgh, Royal (Dick) School of Veterinary Studies, Edinburgh, EH25 9RG UK
| | - James A. Cotton
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA UK
| | - John S. Gilleard
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta Canada
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Deep amplicon sequencing as a powerful new tool to screen for sequence polymorphisms associated with anthelmintic resistance in parasitic nematode populations. Int J Parasitol 2019; 49:13-26. [DOI: 10.1016/j.ijpara.2018.10.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/09/2018] [Accepted: 10/16/2018] [Indexed: 11/17/2022]
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Cole R, Viney M. The population genetics of parasitic nematodes of wild animals. Parasit Vectors 2018; 11:590. [PMID: 30424774 PMCID: PMC6234597 DOI: 10.1186/s13071-018-3137-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/08/2018] [Indexed: 12/17/2022] Open
Abstract
Parasitic nematodes are highly diverse and common, infecting virtually all animal species, and the importance of their roles in natural ecosystems is increasingly becoming apparent. How genes flow within and among populations of these parasites - their population genetics - has profound implications for the epidemiology of host infection and disease, and for the response of parasite populations to selection pressures. The population genetics of nematode parasites of wild animals may have consequences for host conservation, or influence the risk of zoonotic disease. Host movement has long been recognised as an important determinant of parasitic nematode population genetic structure, and recent research has also highlighted the importance of nematode life histories, environmental conditions, and other aspects of host ecology. Commonly, factors influencing parasitic nematode population genetics have been studied in isolation, such that an integrated view of the drivers of population genetic structure of parasitic nematodes is still lacking. Here, we seek to provide a comprehensive, broad, and integrative picture of these factors in parasitic nematodes of wild animals that will be a useful resource for investigators studying non-model parasitic nematodes in natural ecosystems. Increasingly, new methods of analysing the population genetics of nematodes are becoming available, and we consider the opportunities that these afford in resolving hitherto inaccessible questions of the population genetics of these important animals.
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Affiliation(s)
- Rebecca Cole
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK.
| | - Mark Viney
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
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Hodgkinson JE, Cwiklinski K, Beesley N, Hartley C, Allen K, Williams DJL. Clonal amplification of Fasciola hepatica in Galba truncatula: within and between isolate variation of triclabendazole-susceptible and -resistant clones. Parasit Vectors 2018; 11:363. [PMID: 29941045 PMCID: PMC6020221 DOI: 10.1186/s13071-018-2952-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/13/2018] [Indexed: 11/10/2022] Open
Abstract
Background Fasciola hepatica is of worldwide significance, impacting on the health, welfare and productivity of livestock and regarded by WHO as a re-emerging zoonosis. Triclabendazole (TCBZ), the drug of choice for controlling acute fasciolosis in livestock, is also the drug used to treat human infections. However TCBZ-resistance is now considered a major threat to the effective control of F. hepatica. It has yet to be demonstrated whether F. hepatica undergoes a genetic clonal expansion in the snail intermediate host, Galba truncatula, and to what extent amplification of genotypes within the snail facilitates accumulation of drug resistant parasites. Little is known about genotypic and phenotypic variation within and between F. hepatica isolates. Results Six clonal isolates of F. hepatica (3× triclabendazole-resistant, TCBZ-R and 3× triclabendazole-susceptible, TCBZ-S) were generated. Snails infected with one miracidium started to shed cercariae 42–56 days post-infection and shed repeatedly up to a maximum of 11 times. A maximum of 884 cercariae were shed by one clonally-infected snail (FhLivS1) at a single time point, with > 3000 clonal metacercariae shed over its lifetime. Following experimental infection all 12 sheep were FEC positive at the time of TCBZ treatment. Sheep infected with one of three putative TCBZ-S clones and treated with TCBZ had no parasites in the liver at post-mortem, whilst sheep each infected with putative TCBZ-R isolates had 35–165 adult fluke at post-mortem, despite TCBZ treatment. All six untreated control animals had between 15–127 parasites. A single multi-locus genotype was reported for every fluke from each of the six clonal isolates. Adult F. hepatica showed considerable variation in weight, ranging from 20–280 mg, with variation in weight evident within and amongst clonal isolates. Conclusions A genetic clonal expansion occurs within G. truncatula, highlighting the potential for amplification of drug resistant genotypes of F. hepatica. Variation in the weight of parasites within and between clonal isolates and when comparing isolates that are either susceptible or resistant to TCBZ represent inherent variation in liver fluke and cannot be attributed to their resistance or susceptibility traits.
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Affiliation(s)
- Jane E Hodgkinson
- Veterinary Parasitology, Dept Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7ZJ, UK.
| | - Krystyna Cwiklinski
- Veterinary Parasitology, Dept Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7ZJ, UK.,School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, BT9 7BL, UK
| | - Nicola Beesley
- Veterinary Parasitology, Dept Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7ZJ, UK
| | - Catherine Hartley
- Veterinary Parasitology, Dept Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7ZJ, UK
| | - Katherine Allen
- Veterinary Parasitology, Dept Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7ZJ, UK
| | - Diana J L Williams
- Veterinary Parasitology, Dept Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7ZJ, UK
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47
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Zamanian M, Cook DE, Zdraljevic S, Brady SC, Lee D, Lee J, Andersen EC. Discovery of genomic intervals that underlie nematode responses to benzimidazoles. PLoS Negl Trop Dis 2018; 12:e0006368. [PMID: 29601575 PMCID: PMC5895046 DOI: 10.1371/journal.pntd.0006368] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 04/11/2018] [Accepted: 03/05/2018] [Indexed: 01/21/2023] Open
Abstract
Parasitic nematodes impose a debilitating health and economic burden across much of the world. Nematode resistance to anthelmintic drugs threatens parasite control efforts in both human and veterinary medicine. Despite this threat, the genetic landscape of potential resistance mechanisms to these critical drugs remains largely unexplored. Here, we exploit natural variation in the model nematodes Caenorhabditis elegans and Caenorhabditis briggsae to discover quantitative trait loci (QTL) that control sensitivity to benzimidazoles widely used in human and animal medicine. High-throughput phenotyping of albendazole, fenbendazole, mebendazole, and thiabendazole responses in panels of recombinant lines led to the discovery of over 15 QTL in C. elegans and four QTL in C. briggsae associated with divergent responses to these anthelmintics. Many of these QTL are conserved across benzimidazole derivatives, but others show drug and dose specificity. We used near-isogenic lines to recapitulate and narrow the C. elegans albendazole QTL of largest effect and identified candidate variants correlated with the resistance phenotype. These QTL do not overlap with known benzimidazole target resistance genes from parasitic nematodes and present specific new leads for the discovery of novel mechanisms of nematode benzimidazole resistance. Analyses of orthologous genes reveal conservation of candidate benzimidazole resistance genes in medically important parasitic nematodes. These data provide a basis for extending these approaches to other anthelmintic drug classes and a pathway towards validating new markers for anthelmintic resistance that can be deployed to improve parasite disease control. The treatment of roundworm (nematode) infections in both humans and animals relies on a small number of anti-parasitic drugs. Resistance to these drugs has appeared in veterinary parasite populations and is a growing concern in human medicine. A better understanding of the genetic basis for parasite drug resistance can be used to help maintain the effectiveness of anti-parasitic drugs and to slow or to prevent the spread of drug resistance in parasite populations. This goal is hampered by the experimental intractability of nematode parasites. Here, we use non-parasitic model nematodes to systematically explore responses to the critical benzimidazole class of anti-parasitic compounds. Using a quantitative genetics approach, we discovered unique genomic intervals that control drug effects, and we identified differences in the effects of these intervals across compounds and doses. We were able to narrow a major-effect genomic region associated with albendazole resistance and to establish that candidate genes discovered in our genetic mappings are largely conserved in important human and animal parasites. This work provides new leads for understanding parasite drug resistance and contributes a powerful template that can be extended to other anti-parasitic drug classes.
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Affiliation(s)
- Mostafa Zamanian
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Daniel E Cook
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America.,Interdisciplinary Biological Science Program, Northwestern University, Evanston, Illinois, United States of America
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America.,Interdisciplinary Biological Science Program, Northwestern University, Evanston, Illinois, United States of America
| | - Shannon C Brady
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America.,Interdisciplinary Biological Science Program, Northwestern University, Evanston, Illinois, United States of America
| | - Daehan Lee
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America.,Institute of Molecular Biology and Genetics, Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Junho Lee
- Institute of Molecular Biology and Genetics, Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, United States of America.,Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois, United States of America
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48
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Doyle SR, Laing R, Bartley DJ, Britton C, Chaudhry U, Gilleard JS, Holroyd N, Mable BK, Maitland K, Morrison AA, Tait A, Tracey A, Berriman M, Devaney E, Cotton JA, Sargison ND. A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry. Genome Biol Evol 2018; 10:396-409. [PMID: 29267942 PMCID: PMC5793844 DOI: 10.1093/gbe/evx269] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2017] [Indexed: 12/27/2022] Open
Abstract
The parasitic nematode Haemonchus contortus is an economically and clinically important pathogen of small ruminants, and a model system for understanding the mechanisms and evolution of traits such as anthelmintic resistance. Anthelmintic resistance is widespread and is a major threat to the sustainability of livestock agriculture globally; however, little is known about the genome architecture and parameters such as recombination that will ultimately influence the rate at which resistance may evolve and spread. Here, we performed a genetic cross between two divergent strains of H. contortus, and subsequently used whole-genome resequencing of a female worm and her brood to identify the distribution of genome-wide variation that characterizes these strains. Using a novel bioinformatic approach to identify variants that segregate as expected in a pseudotestcross, we characterized linkage groups and estimated genetic distances between markers to generate a chromosome-scale F1 genetic map. We exploited this map to reveal the recombination landscape, the first for any helminth species, demonstrating extensive variation in recombination rate within and between chromosomes. Analyses of these data also revealed the extent of polyandry, whereby at least eight males were found to have contributed to the genetic variation of the progeny analyzed. Triploid offspring were also identified, which we hypothesize are the result of nondisjunction during female meiosis or polyspermy. These results expand our knowledge of the genetics of parasitic helminths and the unusual life-history of H. contortus, and enhance ongoing efforts to understand the genetic basis of resistance to the drugs used to control these worms and for related species that infect livestock and humans throughout the world. This study also demonstrates the feasibility of using whole-genome resequencing data to directly construct a genetic map in a single generation cross from a noninbred nonmodel organism with a complex lifecycle.
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Affiliation(s)
- Stephen R Doyle
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Roz Laing
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - David J Bartley
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
| | - Collette Britton
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Umer Chaudhry
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Alberta, Canada
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Barbara K Mable
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Kirsty Maitland
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Alison A Morrison
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
| | - Andy Tait
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Alan Tracey
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Eileen Devaney
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - James A Cotton
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Neil D Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
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49
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Turnbull F, Jonsson NN, Kenyon F, Skuce PJ, Bisset SA. P-glycoprotein-9 and macrocyclic lactone resistance status in selected strains of the ovine gastrointestinal nematode, Teladorsagia circumcincta. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2018; 8:70-80. [PMID: 29414109 PMCID: PMC6114102 DOI: 10.1016/j.ijpddr.2018.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 01/15/2018] [Accepted: 01/17/2018] [Indexed: 12/05/2022]
Abstract
The Teladorsagia circumcincta P-glycoprotein-9 (Tci-pgp-9) gene has previously been implicated in multiple-anthelmintic resistance in this parasite. Here we further characterise genetic diversity in Tci-pgp-9 and its possible role in ivermectin (IVM) and multi-drug resistance using two UK field isolates of T. circumcincta, one susceptible to anthelmintics (MTci2) and the other resistant to most available anthelmintics including IVM (MTci5). A comparison of full-length Tci-pgp-9 cDNA transcripts from the MTci2 and MTci5 isolates (∼3.8 kb in both cases) indicated that they shared 95.6% and 99.5% identity at the nucleotide and amino acid levels, respectively. Nine non-synonymous SNPs were found in the MTci5 sequences relative to their MTci2 counterparts. Twelve genomic sequence variants of the first internucleotide binding domain of Tci-pgp-9 were identified and up to 10 of these were present in some individual worms, strongly supporting previous evidence that amplification of this gene has occurred in T. circumcincta. On average, fewer distinct sequence variants of Tci-pgp-9 were present in individual worms of the MTci5 isolate than in those of the MTci2 isolate. A further reduction in the number of sequence variants was observed in individuals derived from an IVM-treated sub-population of MTci5. These findings suggest that Tci-pgp-9 was under purifying selection in the face of IVM treatment in T. circumcincta, with some sequence variants being selected against. Tci-pgp-9 cDNA sequences from the MTci2 and MTci5 isolates shared 95.6% identity. Comparison of Tci-pgp-9 sequences from MTci5 and MTci2 showed 9 non-synonymous SNPs. Multiple Tci-pgp-9-IBDA sequence variants occurred in the majority of individual larvae. Tci-pgp-9 appears to be under purifying selection after anthelmintics are applied.
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Affiliation(s)
- Frank Turnbull
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, EH26 0PZ, United Kingdom; Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, United Kingdom.
| | - Nicholas N Jonsson
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Bearsden Road, Glasgow, G61 1QH, United Kingdom
| | - Fiona Kenyon
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, EH26 0PZ, United Kingdom
| | - Philip J Skuce
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh, EH26 0PZ, United Kingdom
| | - Stewart A Bisset
- AgResearch, Hopkirk Research Institute, Palmerston North, 4442, New Zealand
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50
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Gillan V, Maitland K, Laing R, Gu H, Marks ND, Winter AD, Bartley D, Morrison A, Skuce PJ, Rezansoff AM, Gilleard JS, Martinelli A, Britton C, Devaney E. Increased Expression of a MicroRNA Correlates with Anthelmintic Resistance in Parasitic Nematodes. Front Cell Infect Microbiol 2017; 7:452. [PMID: 29209592 PMCID: PMC5701612 DOI: 10.3389/fcimb.2017.00452] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/04/2017] [Indexed: 12/12/2022] Open
Abstract
Resistance to anthelmintic drugs is a major problem in the global fight against parasitic nematodes infecting humans and animals. While previous studies have identified mutations in drug target genes in resistant parasites, changes in the expression levels of both targets and transporters have also been reported. The mechanisms underlying these changes in gene expression are unresolved. Here, we take a novel approach to this problem by investigating the role of small regulatory RNAs in drug resistant strains of the important parasite Haemonchus contortus. microRNAs (miRNAs) are small (22 nt) non-coding RNAs that regulate gene expression by binding predominantly to the 3′ UTR of mRNAs. Changes in miRNA expression have been implicated in drug resistance in a variety of tumor cells. In this study, we focused on two geographically distinct ivermectin resistant strains of H. contortus and two lines generated by multiple rounds of backcrossing between susceptible and resistant parents, with ivermectin selection. All four resistant strains showed significantly increased expression of a single miRNA, hco-miR-9551, compared to the susceptible strain. This same miRNA is also upregulated in a multi-drug-resistant strain of the related nematode Teladorsagia circumcincta. hco-miR-9551 is enriched in female worms, is likely to be located on the X chromosome and is restricted to clade V parasitic nematodes. Genes containing predicted binding sites for hco-miR-9551 were identified computationally and refined based on differential expression in a transcriptomic dataset prepared from the same drug resistant and susceptible strains. This analysis identified three putative target mRNAs, one of which, a CHAC domain containing protein, is located in a region of the H. contortus genome introgressed from the resistant parent. hco-miR-9551 was shown to interact with the 3′ UTR of this gene by dual luciferase assay. This study is the first to suggest a role for miRNAs and the genes they regulate in drug resistant parasitic nematodes. miR-9551 also has potential as a biomarker of resistance in different nematode species.
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Affiliation(s)
- Victoria Gillan
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Kirsty Maitland
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Roz Laing
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Henry Gu
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Neil D Marks
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Alan D Winter
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - David Bartley
- Moredun Research Institute, Pentlands Science Park, Edinburgh, United Kingdom
| | - Alison Morrison
- Moredun Research Institute, Pentlands Science Park, Edinburgh, United Kingdom
| | - Philip J Skuce
- Moredun Research Institute, Pentlands Science Park, Edinburgh, United Kingdom
| | - Andrew M Rezansoff
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Collette Britton
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Eileen Devaney
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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